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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

 

 

FORM 10-K

 

 

Mark One

 

x ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the Fiscal Year Ended December 31, 2008

OR

 

¨ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from             to             .

Commission File No. 001-33093

LIGAND PHARMACEUTICALS INCORPORATED

(Exact name of registrant as specified in its charter)

 

Delaware   77-0160744

(State or other jurisdiction of

incorporation or organization)

 

(IRS Employer

Identification No.)

10275 Science Center Drive

San Diego, CA

  92121-1117
(Address of Principal Executive Offices)   (Zip Code)

Registrant’s telephone number, including area code: (858) 550-7500

Securities registered pursuant to Section 12(b) of the Act:

 

Title of Each Class

  

Name of Each Exchange on Which Registered

Common Stock, par value $.001 per share

   The NASDAQ Global Market of The NASDAQ Stock Market LLC

Preferred Share Purchase Rights

   The NASDAQ Global Market of The NASDAQ Stock Market LLC

Securities registered pursuant to Section 12(g) of the Act:

None

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.    Yes   ¨     No   x

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Securities Exchange Act of 1934.    Yes   ¨     No   x

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes   x     No   ¨

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K.   x

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, or a non-accelerated filer. See definition of “accelerated filer and large accelerated filer” in Rule 12b-2 of the Exchange Act. (Check one):

Large Accelerated Filer   ¨                 Accelerated Filer   x                 Non-accelerated Filer   ¨

Indicate by check mark whether the registrant is a shell company (as defined in Exchange Act Rule 12b-2 of the Exchange Act).    Yes   ¨     No   x

The aggregate market value of the Registrant’s voting and non-voting stock held by non-affiliates was approximately $216.5 million based on the last sales price of the Registrant’s Common Stock on the NASDAQ Global Market of the NASDAQ Stock Market LLC on June 30, 2008. For purposes of this calculation, shares of Common Stock held by directors, officers and 10% stockholders known to the Registrant have been deemed to be owned by affiliates which should not be construed to indicate that any such person possesses the power, direct or indirect, to direct or cause the direction of the management or policies of the Registrant or that such person is controlled by or under common control with the Registrant.

As of February 27, 2009, the Registrant had 113,292,801 shares of Common Stock outstanding.

DOCUMENTS INCORPORATED BY REFERENCE

Portions of the Proxy Statement for the Registrant’s 2009 Annual Meeting of Stockholders to be filed with the Commission on or before April 30, 2009 are incorporated by reference in Part III of this Annual Report on Form 10-K. With the exception of those portions that are specifically incorporated by reference in this Annual Report on Form 10-K, such Proxy Statement shall not be deemed filed as part of this Report or incorporated by reference herein.

 

 

 


Table of Contents

Table of Contents

 

Part I

  

Item 1.

  

Business

   1

Item 1A.

  

Risk Factors

   18

Item 1B.

  

Unresolved Staff Comments

   29

Item 2.

  

Properties

   29

Item 3.

  

Legal Proceedings

   30

Item 4.

  

Submission of Matters to a Vote of Security Holders

   31
  

Executive Officers of the Registrant

   31

Part II

  

Item 5.

  

Market for Registrant’s Common Equity, Related Stockholder Matters, and Issuer Purchases of Equity Securities

   33

Item 6.

  

Selected Consolidated Financial Data

   35

Item 7.

  

Management’s Discussion and Analysis of Financial Condition and Results of Operations

   37

Item 7A.

  

Quantitative and Qualitative Disclosures About Market Risk

   56

Item 8.

  

Consolidated Financial Statements and Supplementary Data

   57

Item 9.

  

Changes in and Disagreements with Accountants on Accounting and Financial Disclosure

   104

Item 9A.

  

Controls and Procedures

   104

Item 9B.

  

Other Information

   106

Part III

  

Item 10.

  

Directors, Executive Officers and Corporate Governance

   106

Item 11.

  

Executive Compensation

   106

Item 12.

  

Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters

   106

Item 13.

  

Certain Relationships and Related Transactions, and Director Independence

   106

Item 14.

  

Principal Accountant Fees and Services

   106

Part IV

  

Item 15.

  

Exhibits and Financial Statement Schedule

   107

SIGNATURES

   120

AVAILABLE INFORMATION:

We file electronically with the Securities and Exchange Commission (or SEC) our annual reports on Form 10-K, quarterly reports on Form 10-Q and current reports on Form 8-K and, as necessary, amendments to these reports, pursuant to Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended. The public may read or copy any materials we file with the SEC at the SEC’s Public Reference Room at 100 F Street, NE, Washington, DC 20549. The public may obtain information on the operation of the Public Reference Room by calling the SEC at 1-800-SEC-0330. The SEC maintains an Internet site that contains reports, proxy and information statements, and other information regarding issuers that file electronically with the SEC. The address of that site is <http://www.sec.gov> .

You may obtain a free copy of our annual reports on Form 10-K, quarterly reports on Form 10-Q and current reports on Form 8-K and amendments to those reports which are posted as soon as reasonably practicable after filing on our website at <http://www.ligand.com> , by contacting the Investor Relations Department at our corporate offices by calling (858) 550-7500 or by sending an e-mail message to investors@ligand.com. You may also request information via the Investor Relations page of our website.


Table of Contents

PART I

 

Item 1. Business

Caution : This discussion and analysis may contain predictions, estimates and other forward-looking statements that involve a number of risks and uncertainties, including those discussed in Item 1A. “Risk Factors.” This outlook represents our current judgment on the future direction of our business. These statements include those related to our AVINZA and PROMACTA royalty revenues, product returns, and product development. Actual events or results may differ materially from Ligand’s expectations. For example, there can be no assurance that our revenues or expenses will meet any expectations or follow any trend(s), that we will be able to retain our key employees or that we will be able to enter into any strategic partnerships or other transactions. We cannot assure you that we will receive expected AVINZA and PROMACTA royalties to support our ongoing business or that our internal or partnered pipeline products will progress in their development, gain marketing approval or achieve success in the market. In addition, our ongoing SEC investigation, or future arbitration, litigation or disputes with third parties may have a material adverse effect on us. Such risks and uncertainties, and others, could cause actual results to differ materially from any future performance suggested. We undertake no obligation to release publicly the results of any revisions to these forward-looking statements to reflect events or circumstances arising after the date of this annual report. This caution is made under the safe harbor provisions of Section 21E of the Securities Exchange Act of 1934, as amended.

References to “Ligand Pharmaceuticals Incorporated”, “Ligand”, the “Company”, “we” or “our” include our wholly owned subsidiaries—Ligand Pharmaceuticals International, Inc.; Seragen, Inc., or Seragen; Pharmacopeia, LLC; and Nexus Equity VI LLC, or Nexus.

We were incorporated in Delaware in 1987. Our principal executive offices are located at 10275 Science Center Drive, San Diego, California, 92121. Our telephone number is (858) 550-7500.

Overview

We are a biotechnology company that focuses on drug discovery and early-stage development of pharmaceuticals that address critical unmet medical needs or that are more effective and/or safer than existing therapies, more convenient to administer and are cost effective. Our goal is to build a profitable company by generating income from research, milestone, and royalty revenues resulting from our collaborations with pharmaceutical partners.

On December 23, 2008, we acquired all of the outstanding common shares of Pharmacopeia, Inc., or Pharmacopeia. As consideration, we issued approximately 18.0 million shares of our common stock to Pharmacopeia stockholders, or approximately 0.60 shares for each outstanding Pharmacopeia share, as well as approximately $9.3 million in cash. Security holders of Pharmacopeia also received contingent value rights, under which they could receive an aggregate cash payment of $15.0 million under certain circumstances. Pharmacopeia was a clinical development stage biopharmaceutical company dedicated to discovering and developing novel small molecule therapeutics to address significant medical needs. Pharmacopeia had a broad portfolio of clinical and preclinical candidates under development internally or by partners.

Our business strategy includes targeted internal drug research and early-stage development capabilities. We believe that we have promising product candidates throughout our internal development programs. We also have research and development collaborations for our product candidates with numerous global pharmaceutical companies. These collaborations include ongoing clinical programs at Bristol-Myers Squibb, or BMS, GlaxoSmithKline, or GSK, Pfizer, Schering-Plough, Wyeth, Cephalon and Celgene. These partnered product candidates are being studied for the treatment of large market indications such as thrombocytopenia, rheumatoid

 

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arthritis, asthma, osteoporosis, menopausal symptoms and Alzheimer’s disease as summarized in the following tables.

Pipeline Overview

 

Marketed

  

Under FDA/EU Review

   Phase III

Chronic Pain –Avinza (King)

   Osteoporosis –Bazedoxifene (Wyeth)    Menopausal symptoms –
Bazedoxifene+Premarin (Wyeth)

ITP –Eltrombopag/Promacta (GSK)

   Osteoporosis –Lasofoxifene (Pfizer)    Hepatitis C –Eltrombopag (GSK)
   ITP –Eltrombopag/Revolade (GSK)    Chronic liver disease –
Eltrombopag (GSK)

Phase II

  

Phase I

   Preclinical/Research

DARA

  

Oncology-related

Thrombocytopenia-Eltrombopag (GSK)

   Alzheimer’s –BACE inhibitor
(Schering)

ITP-LGD-4665 (GSK)

   Leukemia –PS095760 (Schering)    Muscle wasting-LGD-4033
Oncology-related thrombocytopenia –Eltrombopag (GSK)    Inflammation –PS386113 (Schering)    Inflammation-CCR1 antagonist
COPD and Asthma –PS291822 (Schering)    Respiratory-PS948115 (Schering)    Hematological-Erythropoietin
receptor agonist
RA, psoriasis and atherosclerosis –PS540446 (BMS)    Metabolic-PS248288 (Schering)    Inflammation –Selective
glucocorticoid receptor modulator
   Inflammation-PS873266 (Celgene)    Androgen independent prostate
cancer –receptor modulators
   Muscle wasting-PS178990   

Marketed Products

We currently receive royalty revenues from King Pharmaceuticals, or King, and GSK. In February 2007, we completed the sale of our AVINZA product line to King. As a result of the sale, we received the right to future royalties on the net sales of AVINZA through 2017. Through October 2008, we received a 15% royalty on AVINZA net sales. Subsequent royalty payments will be based upon calendar year net sales (see Table 2 below).

In December 2008, the U.S. Food and Drug Administration, or FDA, granted accelerated approval of GSK’s PROMACTA for the treatment of thrombocytopenia in patients with chronic immune (idiopathic) thrombocytopenic purpura, or ITP, who have had an insufficient response to corticosteroids, immunoglobulins or splenectomy. PROMACTA is the first oral thrombopoietin, or TPO, receptor agonist therapy for the treatment of adult patients with chronic ITP. As a result of the FDA’s approval of PROMACTA, we are entitled to receive tiered royalties annual net sales of PROMACTA (Table 2). As part of a settlement agreement and mutual release we entered into on February 12, 2009 with The Rockefeller University, or Rockefeller, we agreed to pay a share of such royalties to Rockefeller. See “Item 3. Legal Proceedings.”

Near-term potential royalties: Products under FDA/EU review and in Phase III

We also have the potential to receive near-term royalties on product candidates resulting from our research and development collaboration arrangements with third party pharmaceutical companies if and when any such product candidate is ultimately approved by the FDA and successfully marketed. Our near-term product candidates are discussed below.

 

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In addition to the accelerated approval granted for GSK’s PROMACTA for the treatment of thrombocytopenia in patients with chronic ITP, GSK also reported positive Phase II data in patients with thrombocytopenia associated with hepatitis C and initiated two Phase III trials in patients with hepatitis C in the fourth quarter of 2007 and a Phase III trial in patients with chronic liver disease (CLD) in early 2008. A Phase II study in patients with oncology-related thrombocytopenia is ongoing and a Phase I study is ongoing in patients with sarcoma receiving the adriamycin and ifosfamide regimen. In December 2008, GSK submitted a marketing authorization application in EU and international for Revolade (Eltrombopag) for the treatment of thrombocytopenia in patients with chronic immune (idiopathic) thrombocytopenic purpura, or ITP (see pipeline overview Table).

Bazedoxifene (Viviant) is a product candidate that resulted from one of our collaborations with Wyeth. Bazedoxifene is a synthetic drug that was specifically designed to reduce the risk of osteoporotic fractures while at the same time protecting breast and uterine tissue. In June 2006, Wyeth submitted an NDA for bazedoxifene to the FDA for the prevention of postmenopausal osteoporosis. Wyeth also submitted a second NDA for bazedoxifene in the United States in July 2007 for the treatment of osteoporosis and a Marketing Authorization Application, or MAA, to the European Medicines Agency, or EMEA, in September 2007 for the prevention and treatment of osteoporosis. Wyeth has indicated that it will file a complete response in 2009 and expects the FDA to convene an advisory committee to review the pending NDAs for both the treatment and prevention of postmenopausal osteoporosis with VIVIANT. In February 2009, CONBRIZA (EU trade name) received positive Committee for Medicinal Products for Human Use (CHMP) opinion in Europe for the treatment of postmenopausal osteoporosis in women at increased risk of fracture

Wyeth is also developing bazedoxifene in combination with PREMARIN (Aprela) as a progesterone-free treatment for menopausal symptoms. Two Phase III studies with bazedoxifene/conjugated estrogens (Aprela), showed reduced number and severity of hot flashes in symptomatic postmenopausal women by up to 80 percent, when compared with placebo. Wyeth expects to file an initial NDA no earlier than the first half of 2010. We are entitled to receive tiered royalties on these products (see Table 2 below).

Lasofoxifene (FABLYN ® ) is a product candidate that resulted from our collaboration with Pfizer. Pfizer submitted an NDA and an MAA for FABLYN for osteoporosis treatment in December 2007 and January 2008, respectively. The FDA Advisory Committee in early September 2008 voted 9-3 in favor of approving this drug. In January 2009, Pfizer received a complete response letter from the FDA requesting additional information for FABLYN. Pfizer is reviewing the letter and will work with the FDA to determine the appropriate next steps regarding its application. In December 2008 CHMP granted a positive opinion for the approval of lasofoxifene in the EU for the treatment of osteoporosis in postmenopausal women at increased risk of fracture. Pfizer has also submitted NDA’s for osteoporosis prevention and vaginal atrophy, and the FDA issued non-approvable letters for both NDA’s. Under the terms of our agreement with Pfizer, we are entitled to receive royalty payments on worldwide net sales of lasofoxifene for any indication. We are entitled to receive royalties on these products (see Table 2 below).

Advanced R&D Programs

PS291822 is a CXCR2 antagonist that resulted from our collaboration with Schering Plough. PS291822 entered Phase II clinical trials in the fourth quarter of 2006 for COPD and asthma. Phase II study in patients with COPD was completed in 4Q 2008. Results from two Phase II studies in asthma are expected later this year.

PS540446 is an orally active p-38 mitogen-activated protein (MAP) kinase inhibitor that resulted from our collaboration with BMS. PS540446 is in Phase II studies for treatment of moderate to severe psoriasis, rheumatoid arthritis (RA) and atherosclerosis. Phase II studies are expected to be complete in 2009. Positive Phase I results in healthy subjects and in patients with stable RA were reported at the 2008 ACR meeting.

DARA (PS433540) is a first-in-class Dual Acting Receptor Agonist (DARA) that targets the angiotensin and endothelin receptors. Given its unique mechanism of action, DARA has the potential to treat diabetic

 

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nephropathy. In connection with our acquisition of Pharmacopeia, Inc., or the Merger, we assumed an exclusive licensing agreement with BMS, whereby we obtained the rights for worldwide development and commercialization of DARA. In February 2009 we announced preliminary results of a Phase IIb study which compared 200 mg, 400 mg, and 800 mg doses of DARA versus placebo and irbesartan for 12-weeks in hypertensive patients. In this study all doses of DARA reduced blood pressure statistically significantly greater than placebo. The 800 mg DARA dose group showed a statistically significantly higher percentage of patients achieving blood pressure control compared to irbesartan. DARA was generally well tolerated and there were no serious adverse events associated with therapy. Ligand plans to pursue discussions with potential collaborators to partner this program based on data received to date.

In December 2008, we entered into an exclusive, worldwide license agreement with SmithKline Beecham Corporation, doing business as GSK. Pursuant to the terms of the GSK agreement, we granted GSK the exclusive right to develop, manufacture and commercialize our LGD-4665 product candidate, as well as all other TPO-related molecules discovered by us. LGD-4665 is currently in a Phase II trial for treatment of thrombocytopenia, a condition of low-platelet levels commonly associated with a diverse range of clinical disorders. Under the terms of the GSK agreement, GSK paid us $5 million as an upfront license fee and agreed to pay us up to $158.0 million in development and commercial milestones and a fixed royalty on net sales (see Table 2 below). We reported at the December 2008 American Society of Hematology annual meeting that LGD-4665 has the potential for weekly dosing, has differentiated clinical pharmacology from other products on the market and has promising potential efficacy in ITP, based on interim clinical study results.

Business Strategy

We aim to create value for shareholders by advancing our internally developed programs through early clinical development and then entering licensing agreements with larger pharmaceutical and biotechnology companies with substantially greater development and commercialization infrastructure. In addition to advancing our R&D programs, we expect to collect licensing fees and royalties from existing and future license agreements. We aim to build a profitable company by generating income from our corporate licenses. The principal elements of our strategy are set forth below.

Leverage Proprietary Gene Expression and Combinatorial Chemistry Platform Technologies Related to Multiple Novel Drug Discovery Programs. Ligand technology applies the most advanced cell-based assays, and gene-expression tools, ultra-high throughput screening and one of the world’s largest chemical libraries to discover new and important medicines:

 

   

Intracellular Technology: Ligand pioneered the field of Intracellular receptor (IR) drug discovery using cell-based assays of nuclear receptors, cell signaling enzymes and membrane receptors. Intracellular receptors are families of transcription factors that change cell function by selectively turning on or off specific genes in response to circulating signals that act on cells. Our ability to harness these processes through IR technology has enabled the development of novel, small-molecule drugs that act through intracellular receptors, potentially resulting in more targeted drugs with greater specificity than those currently available.

 

   

Chemical Library: In December 2008, Ligand acquired high quality combinatorial libraries and proprietary ultra-high through-put screening technology as a result of the acquisition of Pharmacopeia. Our Encoded Combinatorial Library on Polymeric Support, or ECLiPS™, combinatorial library technology provides the power of one of the world’s largest chemical collections to identifying drugs for novel receptor and enzyme drug targets. Ligand uses a proprietary combinatorial compound collection wedded to a unique ultra-high throughput screening platform to drive lead generation for itself and its pharma partners. Our collection of drug-like molecules is built by our chemists on polystyrene beads and ‘encoded’ with molecular tags that can be easily ‘decoded’ for hit identification. This ECLiPS forms the basis for one of the largest compound collections in the industry. Our proprietary tagging technology obviates the usual deconvolution process and facilitates both accurate and rapid hit identification. This combinatorial chemistry collection is built for chemical diversity and drug-like properties. In this way our hits combine the desired target activity with appropriate physicochemical properties that support continued drug discovery.

 

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Ultra-High Throughput Screening: Ligand has married this large proprietary compound collection with industry leading ultra-high throughput screening (UHTS) capacity and capability. More than 70% of our screens are in 1536-well plate formats with well volumes of 1 to 9 microliters. We have developed nanovolume liquid dispensing to deliver reagent volumes as low as 50 nL to 1536 plates with exceptional accuracy. Numerous types of screening and detection capabilities are employed, including cell-free and cell-based, functional or binding, fluorescent or radioactive, and many others.

Discover and Develop Targeted Modulators that are Promising Drug Candidates. We discover, synthesize and test numerous compounds to identify those that are most promising for clinical development. We perform extensive target profiling and base our selection of promising development candidates on product characteristics such as initial indications of safety and efficacy. We believe that this focused strategy allows us to eliminate unpromising candidates from consideration sooner without incurring substantial clinical costs.

License Drug Candidates to Other Parties. We generally plan to advance drug candidates through initial and/or early-stage drug development. For larger disease indications requiring complex clinical trials, our strategy is to license drug candidates to pharmaceutical or biotechnology partners for final development and global marketing. We believe partnerships are a source of development payments, license fees, future milestone payments and royalties. They also may provide considerable resources for late-stage product development, regulatory activities, manufacturing and marketing. We believe that focusing on discovery and early-stage drug development while benefiting from our partners’ proven development and commercialization expertise will reduce our internal expenses and allow us to have a larger number of drug candidates progress to later stages of drug development. However, after establishing a lead product candidate, we are willing to license that candidate during any stage of the development process we determine to be beneficial to the company and to the ultimate development and commercialization of that drug candidate.

Generate Revenue through Partnerships to Fund Our Business and Drive Future Profitability. We have multiple sources of potential license and royalty revenue from existing corporate agreements and we may enter additional partnerships that will provide additional revenue opportunities. We have numerous collaborations that have the potential to generate future royalties for Ligand. The revenue generated from these and future potential collaborations will fund our business and potentially provide profits to our shareholders.

 

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Collaborative Research and Development Programs

We have entered into multiple research and development collaboration arrangements with third party pharmaceutical companies. The commercial terms of such arrangements typically include some combination of the following types of fees: exclusivity fees, technology access fees, technology development fees and research support payments, as well as milestone payments, license or commercialization fees. We may also receive royalties on product candidates resulting from our research and development collaboration arrangements if and to the extent any such product candidate is ultimately approved by the FDA and successfully marketed (see Table 2 for certain royalties).

Table 2: Royalties*

 

Product/Program

  

Partner

  

Royalty

     

Rate

  

Tier

Eltrombopag**

(PROMACTA™)

   GSK   

4.7%

6.6%

7.5%

9.4%

9.3%

  

Less than $100M annual sales

On portion of sales in range of $100M - $200M

On portion of sales in range of $200M - $400M

On portion of sales greater than $400M

On portion of sales greater than $1.5B

LGD-4665**

   GSK    14.5%    All sales (6.5% for first year sales)

Various ongoing GSK

research collaborations

   GSK   

6%***

7%

8%

10%

  

Less than $500M annual sales

On portion of sales in range of $500M - $1B

On portion of sales in range of $1B - $3B

On portion of sales greater than $3B

Avinza

   King    5%   

If sales are less than $200M annually

Higher royalties paid if sales exceed $200M

Bazedoxifene (VIVIANT™)

Basedoxifene (APRELA™)

   Wyeth   

0.5%

1.5%

2.5%

  

Less than $400M annual sales

On portion of sales in range of $400M - $1.0B annually

On portion of sales greater than $1B annually

Lasofoxifene (FABLYN ® )*

   Pfizer    3%    All sales

PS873266

   Celgene    2%    All sales

 

* Royalties from other partnered products not listed are either single or double digit royalties as described under collaborative research and development programs. Not all royalties are disclosed due to confidentiality requirements.
** Net of payments due to The Rockefeller University
*** If GSK exercises its Proof of Concept (PoC) Option for a particular Target, Ligand may continue the development until PoC and receive stepped up royalties ranging from 10% to 14% under the categories of annual sales described above.

Our collaborative research and development programs are discussed below.

GlaxoSmithKline Collaboration

PROMACTA and LGD-4665

In December 2008, the FDA granted accelerated approval of GSK’s PROMACTA ® for the treatment of thrombocytopenia in patients with chronic immune (idiopathic) thrombocytopenic purpura (ITP) who have had an insufficient response to corticosteroids, immunoglobulins or splenectomy. PROMACTA is the first oral TPO receptor agonist therapy for the treatment of adult patients with chronic ITP. As a result of the FDA’s approval of

 

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PROMACTA, we are entitled to receive tiered royalties on annual net sales of PROMACTA (Table 2). As part of a settlement agreement and mutual release we entered into on February 11, 2009 with Rockefeller, we agreed to pay a share of such royalties to Rockefeller. See “Item 3. Legal Proceedings.”

In December 2008, we entered into an exclusive, worldwide license agreement with SmithKline Beecham Corporation, doing business as GSK. Pursuant to the terms of the license agreement, we granted GSK the exclusive right to develop, manufacture and commercialize our LGD-4665 product candidate, as well as all other TPO-related molecules discovered by us. LGD-4665 is currently in a Phase II trial for treatment of thrombocytopenia, a condition of low-platelet levels commonly associated with a diverse range of clinical disorders. Under the terms of the license agreement, GSK paid us $5 million as an upfront license fee and agreed to pay us up to $158.0 million in development and commercial milestones and a royalty on net sales (Table 2). In the first year of sales, royalties will be one-half of the regular royalty rate. GSK has the exclusive right to develop, manufacture and commercialize LGD-4665, as well as other TPO-related molecules discovered by us. GSK will direct all product development and commercialization and will be responsible for all costs going forward for development, patent maintenance and prosecution, and commercialization. We reported at the December 2008 American Society of Hematology annual meeting that LGD-4665 has the potential for weekly dosing, has differentiated clinical pharmacology from other products on the market and has promising potential efficacy in ITP, based on interim clinical study results.

Agreement with Pharmacopeia

In connection with the Merger, we assumed a product development and commercialization agreement, or the GSK Agreement, with SmithKlineBeecham Corporation and Glaxo Group Limited (together “GSK”), which was originally entered into in March 2006. Our role in the alliance with GSK is to identify and advance molecules in chosen therapeutic programs to development stage and, subject to certain provisions in the GSK Agreement, further develop the candidates to clinical “proof of concept” (a demonstration of efficacy in humans). We have agreed not to screen our compound library for other collaborators, or for our own account, against any target we screen under the GSK Agreement for a specified period.

The GSK Agreement provides GSK an exclusive option to license the program which is exercisable at specified points of the development process for each program (up to the point of clinical Proof of Concept). Upon licensing a program, GSK is obligated to conduct preclinical development and/or clinical trials and to commercialize pharmaceutical products resulting from such licensed programs on a worldwide basis. We are entitled to receive success-based milestone payments from GSK, starting in the preclinical research stage, for each drug development program under the alliance. If GSK exercises its Candidate Selection Option for a particular target, GSK is obligated to pay a tiered royalty on the annual net sales of products resulting from a particular target (Table 2). If GSK exercises its Proof of Concept Option for a particular target, Ligand may receive stepped up royalties under the categories of annual sales described in Table 2.

In the event that GSK does not exercise its option to license a program, pursuant to the GSK Agreement we retain all rights to such program and may continue to develop the program and commercialize any products resulting from the program, or we may elect to discontinue the program and/or seek other partners for further development and commercialization. Should we develop or partner such a program and commercialize any products resulting from that program, we are obligated to make success-based milestone payments to GSK and pay royalties to GSK ranging from 3% to 7% of net sales upon the successful commercialization of such products.

We and GSK each have the right to terminate the GSK Agreement in our sole discretion under certain specified circumstances at any time during the term of the GSK Agreement. If we exercise our discretionary termination right at any time during the first five years of the term of the GSK Agreement, under certain circumstances we could be required to refund to GSK a portion of the $15.0 million GSK paid to Pharmacopeia for certain initial discovery activities. Pursuant to the terms of the GSK Agreement, the amount of any such refund will be calculated based upon the date upon which such termination occurs.

 

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We received $15.0 million in connection with initial discovery activities which we are obligated to perform under the GSK agreement. We recorded deferred revenue of approximately $14.5 million associated with these payments, net of the fair value of the warrants described below. We have also earned non-refundable aggregate milestone payments of $3.0 million from GSK related to the identification of six lead compounds. These milestone payments were also recorded as deferred revenue due to our continuing performance obligations under the GSK agreement. The initial research term of the GSK agreement expires in March 2011.

Wyeth Collaborations

Bazedoxifene Program

Bazedoxifene (VIVIANT) is a product candidate that resulted from a collaboration with Wyeth. Bazedoxifene is a synthetic drug that was specifically designed to reduce the risk of osteoporotic fractures while at the same time protecting breast and uterine tissue. In June 2006, Wyeth submitted an NDA for bazedoxifene to the FDA for the prevention of postmenopausal osteoporosis. The FDA issued an approvable letter for bazedoxifene for this indication in April 2007. Wyeth received a second approvable letter in December 2007 and plans to have further discussions with the FDA to discuss the issues raised for the prevention indication. Wyeth also submitted a second NDA for bazedoxifene in the United States in July 2007 for the treatment of osteoporosis and an MAA to EMEA in September 2007 for the prevention and treatment of osteoporosis. Wyeth received a third approvable letter in the second quarter of 2008 for bazedoxifene for the treatment of osteoporosis. In the letter, the FDA requested information similar to that outlined in its approvable letter for bazedoxifene’s NDA for the prevention of postmenopausal osteoporosis issued in December 2007. This included further analyses concerning the incidence of stroke and venous thrombotic events. Wyeth indicated that it will file a complete response in 2009 and expects the FDA will convene an advisory committee to review the pending NDAs for both the treatment and prevention of postmenopausal osteoporosis with VIVIANT. In February 2009, VIVIANT received a positive Committee for Medicinal Products for Human Use (CHMP) opinion in Europe for the treatment of postmenopausal osteoporosis in women at increased risk of fracture.

Wyeth is also developing bazedoxifene in combination with PREMARIN (Aprela) as a progesterone-free treatment for menopausal symptoms. Two Phase III studies with bazedoxifene/conjugated estrogens (Aprela), showed reduced number and severity of hot flashes in symptomatic postmenopausal women by up to 80 percent, when compared with placebo. Wyeth expects to file an initial NDA no earlier than the first half of 2010.

We previously sold to Royalty Pharma AG, or Royalty Pharma, the rights to a total of 3.0% of net sales of bazedoxifene for a period of ten years following the first commercial sale of each product. After giving effect to the royalty sale, we will receive tiered royalties on annual net sales as described in Table 2. Additionally, the royalty owed to Royalty Pharma may be reduced by one third if net product sales exceed certain thresholds across all indications.

JAK3 Program

In connection with the completion of our acquisition of Pharmacopeia, we assumed a research and license agreement with Wyeth, acting through its Wyeth Pharmaceuticals Division, providing for the formation of a new alliance based on our Janus Kinase-3, or JAK3, inhibitor program. The alliance’s goal is to identify, develop and commercialize therapeutic products for the treatment of certain immunological conditions in humans. The agreement was originally entered into in December 2006.

Pursuant to the Wyeth Agreement, we and Wyeth each have certain exclusive rights to develop and commercialize products resulting from the JAK3 program and the alliance. We retain the right to develop and commercialize therapeutic products for the employment of topical administration for treatment of dermatological and ocular diseases and Wyeth has the right to develop therapeutic products for all other indications and routes of delivery. Under the terms of the Wyeth Agreement, we have received an up-front non-refundable $5.0 million cash payment, approximately $6.0 million in quarterly research funding, and a non-refundable milestone

 

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payment of $500 thousand. We may also receive an additional $3.0 million over the remaining portion of the initial three-year research term, which expires in December 2009. In addition, we may receive up to $175.0 million for Wyeth’s achievement of development, regulatory and commercialization milestones. Wyeth will pay to Ligand double digit royalties on the net sales of any products commercialized by Wyeth under the collaboration. Each company is responsible for all development, regulatory, manufacturing and commercialization activities for the products it develops and commercializes in its field. The revenue for this research is recognized on a proportional performance basis, which is expected to approximate straight-line recognition of revenue over the initial three year term of the alliance.

Each of the companies has the right to terminate the Wyeth agreement under certain specified circumstances at any time during the term of the Wyeth agreement. In addition, Wyeth has the right, upon providing us six months’ prior written notice, to terminate the research collaboration and/or the Wyeth agreement in its entirety or in part. Such right to termination would not apply to Wyeth’s obligations with respect to any program developed by the collaboration and licensed by Wyeth. No termination will require us to refund to Wyeth any or all of the cash payments described above.

Pfizer Collaboration

Lasofoxifene (FABLYN) is a product candidate that resulted from our collaboration with Pfizer. In April 2007, Pfizer announced completion of the Postmenopausal Evaluation and Risk Reduction with lasofoxifene, or PEARL, Phase III study with favorable efficacy and safety. Pfizer submitted an NDA and an MAA for osteoporosis treatment in December 2007 and January 2008, respectively. The FDA Advisory Committee in early September 2008 voted 9-3 in favor of approval of this drug and in January 2009, Pfizer received a complete response letter from the FDA requesting additional information for FABLYN. Pfizer is reviewing the letter and will work with the FDA to determine the appropriate next steps regarding its application. In December 2008 an EU Drug Panel granted a positive opinion for the approval of lasofoxifene in the EU for the treatment of osteoporosis in postmenopausal women at increased risk of fracture. Pfizer has also submitted NDA’s for osteoporosis prevention and vaginal atrophy, and the FDA issued non-approvable letters for both NDA’s.

Under the terms of our agreement with Pfizer, we are entitled to receive royalty payments on worldwide net sales of lasofoxifene for any indication. We previously sold to Royalty Pharma the rights to a total of 3% of net sales of lasofoxifene for a period of ten years following the first commercial sale of lasofoxifene. After giving effect to the royalty sale, the amount of net royalties we will receive on annual net sales is described in Table 2.

Schering-Plough Collaboration

1998 Collaboration

In connection with our acquisition of Pharmacopeia, we assumed collaboration and license agreements with Schering-Plough Ltd. and Schering Corporation (collectively “Schering-Plough”) that were originally entered into in October of 1998. These agreements produced a CXCR2 antagonist that entered Phase II clinical trials in the fourth quarter of 2006 for COPD and asthma, an enzyme inhibitor that entered Phase II clinical trials in November 2008 for oncology, a candidate for inflammatory diseases that entered Phase I clinical trials in March 2007, a candidate for respiratory diseases that entered Phase I clinical trials in September 2007 and a BACE inhibitor for Alzheimer’s disease for which a first development milestone was achieved in December 2008. Under the terms of these agreements with Schering-Plough, while our research activities have ceased, the cessation of those research activities did not affect other aspects of those agreements, including the ongoing Phase II and Phase I clinical trials and preclinical programs that Schering-Plough is conducting. We continue to be entitled to payments resulting from the successful achievement by Schering-Plough of clinical and regulatory milestones, as well as royalty payments at different rates depending on the origin of collaboration products from discovery and optimization libraries at Ligand and Schering-Plough, and on net sales of products resulting from compounds being developed by Schering-Plough under those agreements.

 

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2007 Collaboration

In connection with our acquisition of Pharmacopeia, we also assumed an amended and restated collaboration and license agreement with N.V. Organon, entered into in February 2007. In November 2007, Organon was acquired by, and is now a part of, Schering-Plough. Under the 2007 Schering-Plough agreement, we have agreed to work collaboratively with Schering-Plough to generate lead compounds at targets in mutual therapeutic areas selected by Schering-Plough and agreed upon by a joint research committee. The purpose of the agreement is to produce development-ready compounds, the potential development of which will be handled primarily by Schering-Plough. The 2007 Schering-Plough agreement provides that we will receive up to $4.0 million per year from Schering-Plough in research funding over the remaining portion of the five-year term of the agreement.

Pursuant to the 2007 Schering-Plough agreement, we have the option to purchase the right to co-develop and co-commercialize certain therapeutic candidates of mutual interest discovered through the alliance. For the therapeutic candidates that we do not elect to co-develop and co-commercialize, Schering-Plough will retain exclusive development and commercialization rights, and we will receive milestone payments as a result of Schering-Plough’s successful advancement, if any, of each candidate through clinical development. We will also receive up to double-digit royalties on net sales, if any, of pharmaceutical products resulting from the collaboration when the lead optimization was conducted by us, and lower royalties when the lead optimization was conducted by Schering-Plough.

We and Schering-Plough each have the right to terminate the 2007 Schering-Plough agreement at any time during the term of the agreement under certain specified circumstances, and upon other circumstances customary for these types of agreements.

Bristol-Myers Squibb Collaborations

P-38 Kinase Program

In connection with the Merger, we assumed a collaboration and license agreement with BMS which was originally entered into in November 1997. This collaboration has resulted in a compound that entered Phase II clinical trials in September 2007 in psoriasis. BMS has also initiated Phase II clinical trials with this compound targeting rheumatoid arthritis and atherosclerosis. A second compound resulting from that partnership, which is a back-up candidate, entered Phase I clinical trials in Canada in December 2005. The research collaboration portion of the agreement has expired, however we will continue to be entitled to payments resulting from the successful achievement by BMS of certain clinical and regulatory milestones, as well as a royalty on net sales of products resulting from compounds already delivered under the agreement.

Medicinal Chemistry Services

In connection with the Merger, we also assumed a discovery collaboration agreement with BMS, or the Discovery Collaboration Agreement, to provide a portion of our medicinal chemistry resources to a BMS discovery program for a period up to three years beginning in October 2007. The Discovery Collaboration Agreement provides that each such year, we are required to provide a fixed number of full-time workers for the BMS discovery program, divided between employees located in Cranbury, New Jersey and contracted headcount located outside the United States.

 

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Cephalon Collaboration

In connection with the Merger, we assumed a collaboration and license agreement, or the Cephalon Agreement, with Cephalon, Inc., or Cephalon, originally entered into in May 2006, which provides for the formation of a new drug discovery, development and commercialization alliance. Under the Cephalon agreement, Pharmacopeia received an up-front, non-refundable payment of $15.0 million in June 2006 to support its research efforts.

Pursuant to the terms of the Cephalon Agreement, Cephalon is responsible for identifying hit and lead compounds, after which we and Cephalon agreed to work together to develop related clinical candidates. We are principally responsible for medicinal chemistry research and Cephalon is responsible for providing biology support, including preclinical disease models, as required by the Cephalon Agreement. We have agreed that, for a specified period, we will not screen our compound library for other collaborators, or for our own account, against any target upon which we collaborate under the Cephalon Agreement.

Upon the nomination of any clinical candidates by the alliance, Cephalon will be primarily responsible for their development and commercialization. We retain an option to develop certain candidates from the alliance, subject to Cephalon’s agreement. For each clinical candidate advanced under the alliance, the developing company is obligated to make clinical, regulatory and sales milestone payments to the non-developing company. In addition, the company commercializing each resulting product is required to pay the non-commercializing company up to a double-digit royalty based on the sales level achieved

In connection with the acquisition of Pharmacopeia, Ligand and Cephalon executed an amendment in January 2009 to the collaboration agreement dated May 16, 2006. The agreement provided for Ligand to have no obligation to continue research activities with respect to the two active collaboration programs and was released to redeploy FTEs currently assigned to the collaboration. All licenses granted to Pharmacopeia by Cephalon with respect to the two active collaboration programs terminated as of the date of amendment. Ligand will be entitled to milestone and royalty payments associated with only one of the two active programs. In addition, Ligand entered in to an agreement with a third party vendor to provide certain chemistry services to Cephalon for a term of nine months from the date of agreement.

We and Cephalon each have the right to terminate the Cephalon agreement under certain specified circumstances at any time during the term of the agreement. In addition, Cephalon has the right to terminate the agreement, in its sole discretion, upon ninety days written notice to us, during the initial three-year phase of the alliance, which phase may be extended by agreement of the parties. No such termination shall require us to refund to Cephalon any or all of the above research and development funding.

Celgene Collaboration

In connection with the Merger, we assumed a research and license agreement, or the Celgene Agreement, with Celgene Corporation, or Celgene. Under the Celgene Agreement we have no further research requirements. Our relationship with Celgene produced a compound that led to a clinical candidate currently being evaluated for the treatment of fibrotic and inflammatory diseases that entered a Phase I clinical trial in the first quarter of 2008. We are entitled to receive payments resulting from the successful achievement by Celgene of clinical milestones, as well as royalties on net sales of products resulting from the collaboration (Table 2).

Trevena Collaboration

In February 2009 Ligand announced the initiation of a joint research and license alliance to screen targets using Trevena’s novel biological platform against Ligand’s combinatorial library of compounds, to identify active compounds with potential for development as novel G-protein coupled receptor (GPCR) therapeutics.

 

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Under the terms of the agreement, Trevena has been granted exclusive worldwide rights to sublicense active compounds resulting from the collaboration. Ligand expects to screen 24 targets over two years and receive payments triggered by a tiered screening paradigm for each target.

Internal Product Development Programs

As summarized in the table below, we are developing several proprietary products for a variety of indications.

 

Program

  

Disease/Indication

   Development Phase
Dual-Acting angiotensin and endothelin Receptor Antagonist (DARA)    Diabetic Nephropathy*    Phase II
Selective Androgen Receptor Modulators (SARMs) (agonists)    Muscle wasting and frailty    Pre-clinical
Chemokine Receptor (CCR1) antagonist    Inflammatory and autoimmune diseases    Pre-clinical
Small molecule Erythropoiein (EPO) receptor agonists    Chemotherapy-induced anemia, anemia due to kidney failure    Research
Selective Glucocorticoid Receptor Modulators (SGRMs)    Inflammation, cancer    Research
Androgen-independent Prostate Cancer (AiPC)    Prostate cancer    Research

 

* Phase II clinical trials conducted so far have studied patients with hypertension

Dual-Acting Angiotensin and Endothelin Receptor Antagonist (DARA) Program

In connection with the completion of our previously announced acquisition of Pharmacopeia, Inc. (the “Merger”), we assumed an exclusive licensing agreement, or the DARA License Agreement, with BMS, originally entered into in March 2006, which provides us with an exclusive license under certain BMS patents with respect to worldwide development and commercialization of DARA (PS433540), as well as certain other compounds discovered by BMS that possess dual angiotensin and endothelin receptor antagonist, or DARA, activity.

DARA has been studied in seven Phase I and two Phase II clinical studies, including a Phase II study in hypertensive patients. Given the drug’s unique mechanism targeting the angiotensin and endothelin receptors, we beleive the drug has potential as a treatment for diabetic nephropathy. In May 2008, results were announced for a Phase IIa study of DARA in subjects with Stage I and Stage II hypertension that showed statistically significantly greater blood pressure reductions than placebo. This study met its primary endpoint by showing a statistically significant effect on 24-hour systolic ambulatory blood pressure and also showed statistically significant improvements over placebo in mean 24-hour diastolic ambulatory blood pressure as well as seated blood pressure. There were no serious adverse events in subjects treated with DARA. Three subjects discontinued therapy for adverse events, all of whom were in the placebo group.

In February 2009, we announced preliminary results of a Phase IIb study of DARA which compared 200 mg , 400 mg, and 800 mg doses of PS433540 versus placebo and irbesartan for 12-weeks in hypertensive patients. In this study all doses of DARA reduced blood pressure statistically significantly greater than placebo. The highest dose of DARA (800 mg) showed a statistically significantly higher percentage of patients achieving blood pressure control compared to irbesartan. DARA was generally well tolerated and there were no serious adverse

 

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events associated with therapy. Ligand plans to pursue discussions with potential collaborators to partner this program based on data received to date.

Under the terms of the DARA License Agreement, we are obligated to pay BMS milestone payments upon the achievement, if any, of further successive clinical and regulatory events in the United States and certain other jurisdictions, and a stepped royalty based on net sales of products, if any, resulting from the DARA program. BMS has a limited right of first negotiation in the event that we desire to license compounds that are the subject of the DARA License Agreement to a third party other than BMS.

In addition, we are required to provide BMS with a set of compound libraries over a period of approximately three years ending in March 2009. In the event we fail to deliver such compound libraries to BMS by the end of March 2010, we could be required to make cash payments to BMS of up to $0.1 million. We expect to complete delivery of these compound libraries by the end of the first quarter of 2009

Selective Androgen Receptor Modulators (SARM) Research and Development Programs

We are developing tissue selective androgen receptor modulators, or SARMs, a novel class of non-steroidal, orally active molecules that selectively modulate the activity of the androgen receptor in different tissues, providing a wide range of opportunities for the treatment of many diseases and disorders in both men and women. Tissue-selective androgen receptor agonists may provide utility in the treatment of patients with frailty, cachexia, osteoporosis, sexual dysfunction and hypogonadism.

We have assembled an extensive SARM compound library and, we believe, one of the most experienced androgen receptor drug discovery teams in the pharmaceutical industry. We may pursue the specialty applications emerging from SARMs internally and seek collaborations with major pharmaceutical companies to exploit broader clinical applications.

LGD-2941, a SARM, was selected as a clinical candidate during our collaboration with TAP. TAP assigned the current SARM agreement to Abbott in the second quarter of 2008 upon the closing of the transaction between Takeda and Abbott to separate portions of the TAP business between the two parties. As part of our joint development and research alliance with TAP Pharmaceutical Products, Inc., or TAP), we exercised an option to select for development one compound and a back-up, LGD-3303 and LGD-3129, respectively, out of a pool of compounds available for development. Preclinical studies we have conducted with LGD-3303 indicate that the compound may have utility for osteoporosis, sexual dysfunction, frailty and hypogonadism. In vivo studies in rodents indicate a favorable profile with anabolic effects on bone, but an absence of the prostatic hypertrophy that occurs with the currently marketed androgens.

After the conclusion of our research alliance with TAP, we discovered SARM compounds with androgen effects in bone and skeletal muscle, but with little or no activity in the prostate, oil-secreting glands in the skin, or female genitalia. Preclinical studies conducted on one of these compounds, LGD-4033, suggest that the compound may have favorable activity in the treatment of cachexia, frailty, osteoporosis, hypogonadism as well as other disorders. We filed an Investigational New Drug (IND) in December 2008 for LGD-4033.

In connection with the acquisition of Pharmacopeia, we assumed an exclusive licensing agreement, or the SARM License Agreement, with BMS, originally entered into in October 2007, which provides us exclusive worldwide development and commercialization rights to a third lead non-steroidal SARM, PS178990, for which a Phase I single ascending dose study had been completed. Under the SARM License Agreement, we are required to make milestone payments to BMS upon the submission and approval of a therapeutic product for marketing in the United States and certain other jurisdictions. BMS has a limited right of first negotiation for PS178990 in the event that we attempt to license compounds that are the subject of the SARM License Agreement to a third party other than BMS.

 

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Chemokine Receptor (CCR1) program

In February 2008, we announced the nomination of PS031291 as a preclinical development compound from our internal chemokine receptor CCR1 program. PS031291 is a potent and highly selective antagonist at the chemokine receptor CCR1, which has been implicated in playing a significant role in multiple inflammatory and autoimmune disease processes. We believe PS031291 may possess significant potential in the treatment of various inflammatory diseases including rheumatoid arthritis. We initiated good laboratory practice (often referred to as GLP) toxicology studies on PS031291 in the second quarter of 2008, and those studies are ongoing.

Erythropoiein (EPO) Research Program

We are developing small molecule agonists for the EPO receptor. EPO stimulates the differentiation of bone marrow stem cells to form red blood cells. Various recombinant human EPO derivatives are marketed for the treatment of anemia due to renal failure or cancer chemotherapy (e.g., Aranesp, Epogen, Eprex, and Procrit). We believe that a small molecule agonist for the EPO receptor would provide additional benefit in the treatment of anemia and the convenience of oral administration compared to recombinant human protein therapeutics. EPO and TPO act on the same bone marrow hematopoietic stem cell to guide the development of blood cells. We expect that our prior experience in developing small molecule TPO mimetic drugs will lead to increased efficiency in discovering small molecule EPO mimetic drugs.

Selective Glucocorticoid Receptor Modulators (SGRM) Research and Development Program

We are developing SGRMs for inflammation, cancer indications and other therapeutic applications. We have a library of compounds that we are optimizing with the goal to identify one or more compounds to enter human trials. Our studies of these compounds are in the research stage.

Androgen-Independent Prostate Cancer (AiPC) program

AiPC typically occurs within two years of initiation of hormonal therapy and no targeted treatment is currently available. Docetaxel is the current standard of care which could extend survival by approximately six months (from 12 to 18 months). Most prostate-derived tumors are initially androgen dependent and they regress in response to androgen ablation therapy. On average, regression lasts about two years, followed by break-through growth of androgen-independent tumors. There is experimental evidence that these androgen-independent tumors require the androgen receptor, or AR, for continued proliferation (i.e. tumors are receptor dependent). The goal of the AiPC program is to identify compounds that specifically inhibit and degrade the AR. Our studies of these compounds are in the research stage.

Technology

We employ various modern research laboratory methods to discover and conduct preclinical development of new chemical entities. These methods are performed either in our own laboratories or in those of contract research organizations under our direction.

In our efforts to discover new and important medicines, we have concentrated on certain technologies and acquired special expertise related to intracellular receptors and the receptors for hematopoietic growth factors. Intracellular receptors are involved in the actions of non-peptide hormones and drugs such as selective androgen receptor modulators, or SERMs, and SARMs. Hematopoietic growth factor receptors are involved in the differentiation and proliferation of blood cell progenitors, the formation of new blood cells, and the action of drugs such as PROMACTA, Epogen and Neumega. We use and have developed particular expertise in co-transfection assays, which measure gene transcription in response to the activation of a target receptor, and gene expression in cells selected for expression of particular receptors or transfected with cDNA for particular receptors. Some of these methods are covered by patents issued to or licensed by Ligand, are trade secrets, or are

 

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methods that are in the public domain, but that we may use in novel ways to improve our efficiency in identifying promising leads and developing new chemical entities.

Our drug discovery approach is further supported by our proprietary combinatorial chemistry encoding technology, Encoded Combinatorial Libraries on Polymeric Support, or ECLiPS ® , our proprietary collection of chemical compounds, assay technology, production automation, information systems and quality assurance programs. We have employed ECLiPS ® , together with other technologies, to assemble what we believe is the largest group of compound libraries held by one company in the pharmaceutical industry. Our small molecule libraries have been engineered to be both drug-like and diverse. Our compound collection and high throughput screening technologies have been proven to be effective against a wide variety of biological targets. Importantly, we have achieved success against some of our collaborators’ most difficult targets, often after our partners’ internal drug discovery efforts were unsuccessful.

Our tagging technology used in ECLiPS ® has been licensed exclusively from the Trustees of Columbia University, or Columbia, and Cold Spring Harbor Laboratory, or Cold Spring, since 1993. We are obligated to pay a minimum annual license fee of $100,000 to Columbia and Cold Spring. The term of the agreement is the later of (i) July 16, 2013 or (ii) the expiration of the last patent relating to the technology, at which time we will have a fully paid license to the technology. The license granted to us under the agreement can be terminated by Columbia and Cold Spring (i) upon 30 days written notice to us if we materially breach the agreement and we fail to cure such material breach in accordance with the agreement or (ii) if we commit any act of bankruptcy, become insolvent, file a petition under any bankruptcy or insolvency act or have any such petition filed against us that is not dismissed within 60 days. We are also obligated to pay royalties to Columbia and Cold Spring based on net sales of pharmaceutical products we develop, as well as a percentage of all other revenue we recognize from collaborators that is derived from the technology licensed from Columbia and Cold Spring.

Manufacturing

We currently have no manufacturing facilities and, accordingly, rely on third parties, including our collaborative partners, for clinical production of any products or compounds.

Sale of Commercial Businesses

In February 2007, we completed the sale of our AVINZA product line to King Pharmaceuticals, Inc, or King. Pursuant to the AVINZA purchase agreement, King acquired all of our rights in and to AVINZA in the United States, its territories and Canada, including, among other things, all AVINZA inventory, records and related intellectual property, and assumed certain liabilities as set forth in the AVINZA purchase agreement. Pursuant to the AVINZA purchase agreement, we received a total of $295.4 million in net cash proceeds. We also received the right to future royalties on the net sales of AVINZA through 2017.

In October 2006, we completed the sale of our Oncology product line to Eisai Inc., a Delaware corporation, and Eisai Co., Ltd., a Japanese company, which we collectively refer to as Eisai. Pursuant to the Oncology purchase agreement, Eisai acquired all of our worldwide rights in and to our oncology products, including, among other things, all related inventory, equipment, records and intellectual property, and assumed certain liabilities as set forth in the Oncology purchase agreement. The Oncology product line included our four marketed oncology drugs: ONTAK, Targretin capsules, Targretin gel and Panretin gel. Pursuant to the Oncology purchase agreement, we received a total of $205.0 million in net cash proceeds.

For further discussion of these items, see below under “Item 7. Management’s Discussion and Analysis of Financial Condition and Results of Operations.”

 

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Research and Development Expenses

Research and development expenses from continuing operations were $30.8 million, $44.6 million, and $41.5 million in 2008, 2007 and 2006, respectively, of which 100%, 100%, and 95%, respectively, were sponsored by us.

Research and development expenses from discontinued operations were none, $0.1 million, and $13.3 million in 2008, 2007 and 2006 respectively.

Competition

Some of the drugs we are developing may compete with existing therapies or other drugs in development by other companies. A number of pharmaceutical and biotechnology companies are pursuing IR-related approaches to drug discovery and development. Furthermore, academic institutions, government agencies and other public and private organizations conducting research may seek patent protection with respect to potentially competing products or technologies and may establish collaborative arrangements with our competitors.

Many of our existing or potential competitors, particularly large pharmaceutical companies, have greater financial, technical and human resources than we do and may be better equipped to develop, manufacture and market products. Many of these companies also have extensive experience in preclinical testing and human clinical trials, obtaining FDA and other regulatory approvals and manufacturing and marketing pharmaceutical products.

Our competitive position also depends upon our ability to attract and retain qualified personnel, obtain patent protection or otherwise develop proprietary products or processes, and secure sufficient capital resources for the often substantial period between technological conception and commercial sales. For a discussion of the risks associated with competition, see below under “Item 1A. Risk Factors.”

Government Regulation

The manufacturing and marketing of our products, our ongoing research and development activities and products being developed by our collaborative partners are subject to regulation for safety and efficacy by numerous governmental authorities in the United States and other countries. In the United States, pharmaceuticals are subject to rigorous regulation by federal and various state authorities, including the FDA. The Federal Food, Drug and Cosmetic Act and the Public Health Service Act govern the testing, manufacture, safety, efficacy, labeling, storage, record keeping, approval, advertising and promotion of our products. There are often comparable regulations that apply at the state level. Product development and approval within this regulatory framework takes a number of years and involves the expenditure of substantial resources.

The steps required before a pharmaceutical agent may be marketed in the United States include (1) preclinical laboratory tests, (2) the submission to the FDA of an IND, which must become effective before human clinical trials may commence, (3) adequate and well-controlled human clinical trials to establish the safety and efficacy of the drug, (4) the submission of an NDA to the FDA and (5) the FDA approval of the NDA prior to any commercial sale or shipment of the drug. In addition to obtaining FDA approval for each product, each domestic drug-manufacturing establishment must be registered with the FDA and, in California, with the Food and Drug Branch of California. Domestic manufacturing establishments are subject to pre-approval inspections by the FDA prior to marketing approval, then to biennial inspections, and must comply with current Good Manufacturing Practices (cGMP). To supply products for use in the United States, foreign manufacturing establishments must comply with cGMP and are subject to periodic inspection by the FDA or by regulatory authorities in such countries under reciprocal agreements with the FDA.

For both currently marketed and future products, failure to comply with applicable regulatory requirements after obtaining regulatory approval can, among other things, result in the suspension of regulatory approval, as well as possible civil and criminal sanctions. In addition, changes in existing regulations could have a material adverse effect to us.

 

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For marketing outside the United States before FDA approval to market, we must submit an export permit application to the FDA. We also are subject to foreign regulatory requirements governing human clinical trials and marketing approval for drugs. The requirements relating to the conduct of clinical trials, product licensing, pricing and reimbursement vary widely from country to country and there can be no assurance that we or any of our partners will meet and sustain any such requirements.

We are also increasingly subject to regulation by the states. A number of states now regulate, for example, pharmaceutical marketing practices and the reporting of marketing activities, controlled substances, clinical trials and general commercial practices. We have developed and are developing a number of policies and procedures to ensure our compliance with these state laws, in addition to the federal regulations described above. Significant resources are now required on an ongoing basis to ensure such compliance. For a discussion of the risks associated with government regulations, see below under “Item 1A. Risk Factors.”

Patents and Proprietary Rights

We believe that patents and other proprietary rights are important to our business. Our policy is to file patent applications to protect technology, inventions and improvements to our inventions that are considered important to the development of our business. We also rely upon trade secrets, know-how, continuing technological innovations and licensing opportunities to develop and maintain our competitive position.

Royalties we currently receive from King on AVINZA represent a significant portion of our ongoing revenue. The United States patent on AVINZA expires in November 2017; however, an application for a generic form of AVINZA has been submitted to the FDA. The United States patents relating to PROMACTA do not expire until December 2021. Subject to compliance with the terms of the respective agreements, our rights under our licenses with our exclusive licensors extend for the life of the patents covering such developments. For a discussion of the risks associated with patent and proprietary rights, see below under “Item 1A. Risk Factors.”

Human Resources

As of February 27, 2009, we had 96 full-time employees, of whom 73 are involved directly in scientific research and development activities. Of these employees, 39 hold Ph.D. or M.D. degrees.

 

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Item 1A.  Risk Factors

The following is a summary description of some of the many risks we face in our business. You should carefully review these risks in evaluating our business, including the businesses of our subsidiaries. You should also consider the other information described in this report.

Risks Related To Us and Our Business.

We are substantially dependent on AVINZA and PROMACTA royalties for our revenues.

King is obligated to pay us royalties based on its sales of AVINZA and GSK is obligated to pay us royalties on its sales of PROMACTA. These royalties represent and will for some time represent substantially all of our ongoing revenue. Although we may also receive royalties and milestones from our partners in various past and future collaborations, the amount of revenue from such royalties and milestones is unknown and highly uncertain. As a result, any setback that may occur with respect to AVINZA or PROMACTA could significantly impair our operating results and/or reduce the market price of our stock. Setbacks could include problems with shipping, distribution, manufacturing, product safety, marketing, government licenses and approvals, intellectual property rights, competition with existing or new products and physician or patient acceptance of the products, as well as higher than expected total rebates, returns or discounts.

King and GSK’s sales efforts for AVINZA and PROMACTA, respectively, could be affected by a number of factors and decisions regarding their organizations, operations, and activities as well as events both related and unrelated to AVINZA or PROMACTA, including sales force reorganizations and lower than expected sales calls and prescription volumes. AVINZA and PROMACTA could also face stiffer competition from existing or future products. The negative impact on the sales of AVINZA or PROMACTA will negatively affect our royalties, revenues and earnings.

Sales of AVINZA and PROMACTA may also be negatively impacted by higher than expected discounts (especially pharmacy benefit management/group purchasing organization rebates and Medicaid rebates, which can be substantial), returns and chargebacks and/or slower than expected market penetration. Other setbacks that AVINZA could face in the sustained-release opioid market include abuse issues and the inability to obtain sufficient quotas of morphine from the Drug Enforcement Agency to support production requirements.

AVINZA or PROMACTA could also face regulatory action and product safety issues. For example, the FDA previously requested expanded warnings on the AVINZA label to alert doctors and patients to the dangers of using AVINZA with alcohol. Changes were subsequently made to the label. The FDA also requested clinical studies to investigate the risks associated with taking AVINZA with alcohol. Any additional warnings, studies and any further regulatory action could have significant adverse effects on AVINZA sales.

On September 10, 2007, King reported that Actavis, a manufacturer of generic pharmaceutical products headquartered in Iceland, had filed with the FDA an Abbreviated New Drug Application, or ANDA, with a Paragraph IV Certification pertaining to AVINZA, the rights to which were acquired by King from us in February 2007. According to the report, Actavis’s Paragraph IV Certification sets forth allegations that U.S. Patent No. 6,066,339, or the 339 patent, which pertains to AVINZA, and which is listed in the FDA’s Approved Drug Products With Therapeutic Equivalence Evaluations, will not be infringed by Actavis’s manufacture, use, or sale of the product for which the ANDA was submitted. The expiration date for this patent is November 2017. King, King Pharmaceuticals Research and Development, Inc., Elan Corporation, plc and Elan Pharma International Ltd. jointly filed suit in federal district court in New Jersey on October 18, 2007 against Actavis, Inc. and Actavis Elizabeth LLC for patent infringement under the 339 patent. The lawsuit seeks a judgment that would, among other things, prevent Actavis from commercializing its proposed morphine product until after expiration of the 339 patent.

 

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AVINZA was licensed from Elan Corporation, or Elan, which is its sole manufacturer. Any problems with Elan’s manufacturing operations or capacity could reduce sales of AVINZA, as could any licensing or other contract disputes with Elan, raw materials suppliers, or others.

Further, pursuant to the agreement with King, beginning in 2009 we will no longer be entitled to receive AVINZA royalties on a quarterly basis, but will collect royalties on an annual basis, which may adversely impact our cash flows.

Our product candidates face significant regulatory hurdles prior to marketing which could delay or prevent sales.

Before we obtain the approvals necessary to sell any of our potential products, we must show through preclinical studies and human testing that each product is safe and effective. We and our partners have a number of products moving toward or currently awaiting regulatory action, including bazedoxifene, lasofoxifene, PS433540 and PS178990. Failure to show any product’s safety and effectiveness could delay or prevent regulatory approval of a product and could adversely affect our business. The clinical trials process is complex and uncertain. For example, the results of preclinical studies and initial clinical trials may not necessarily predict the results from later large-scale clinical trials. In addition, clinical trials may not demonstrate a product’s safety and effectiveness to the satisfaction of the regulatory authorities. Recently, a number of companies have suffered significant setbacks in advanced clinical trials or in seeking regulatory approvals, despite promising results in earlier trials. The FDA may also require additional clinical trials after regulatory approvals are received. Such additional trials may be expensive and time-consuming, and failure to successfully conduct those trials could jeopardize continued commercialization of a product.

The rate at which we complete our clinical trials depends on many factors, including, but not limited to, our ability to obtain adequate supplies of the products to be tested and patient enrollment. Patient enrollment is a function of many factors, including the size of the patient population, the proximity of patients to clinical sites and the eligibility criteria for the trial. Delays in patient enrollment for our trials may result in increased costs and longer development times. In addition, our collaborative partners have rights to control product development and clinical programs for products developed under the collaborations. As a result, these collaborative partners may conduct these programs more slowly or in a different manner than expected. Moreover, even if clinical trials are completed, we or our collaborative partners still may not apply for FDA approval in a timely manner or the FDA still may not grant approval.

We rely heavily on collaborative relationships, and any disputes or litigation with our collaborative partners or termination or breach of any of the related agreements could reduce the financial resources available to us, including milestone payments and future royalty revenues.

Our strategy for developing and commercializing many of our potential products, including products aimed at larger markets, includes entering into collaborations with corporate partners and others. These collaborations have provided us with funding and research and development resources for potential products for the treatment of a variety of diseases. These agreements also give our collaborative partners significant discretion when deciding whether or not to pursue any development program. Our existing collaborations may not continue or be successful, and we may be unable to enter into future collaborative arrangements to develop and commercialize our product candidates.

In addition, our collaborators may develop drugs, either alone or with others that compete with the types of drugs they are developing with us. This would result in increased competition for our programs. If products are approved for marketing under our collaborative programs, revenues we receive will depend on the manufacturing, marketing and sales efforts of our collaborative partners, who generally retain commercialization rights under the collaborative agreements. Generally, our current collaborative partners also have the right to terminate their collaborations under specified circumstances. If any of our collaborative partners breach or

 

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terminate their agreements with us or otherwise fail to conduct their collaborative activities successfully, our product development under these agreements will be delayed or terminated. Disputes or litigation may also arise with our collaborators, including disputes or litigation over ownership rights to intellectual property, know-how or technologies developed with our collaborators. Such disputes or litigation could adversely affect our rights to one or more of our product candidates, including our PS433540, PS178990 and LGD-4665 and other small-molecule TPO mimetic compounds. Any such dispute or litigation could delay, interrupt or terminate the collaborative research, development and commercialization of certain potential products, create uncertainty as to ownership rights of intellectual property, or could result in litigation or arbitration. The occurrence of any of these problems could be time-consuming and expensive and could adversely affect our business.

If we consume cash more quickly than expected, and if we are unable to raise additional capital, we may be forced to curtail operations.

Our operations have consumed substantial amounts of cash since inception. Clinical and preclinical development of drug candidates is a long, expensive and uncertain process. Also, we may acquire companies, businesses or products and the consummation of such acquisitions may consume additional cash. For example, as part of the consideration for our recent acquisition of Pharmacopeia we distributed approximately $9.3 million in cash to Pharmacopeia stockholders. Security holders of Pharmacopeia also received contingent value rights under which we could be required to make an aggregate cash payment of $15.0 million to such security holders under certain circumstances.

We believe that our capital resources will be adequate to fund our operations at their current levels at least for the next twelve months. However, changes may occur that would cause us to consume available capital resources before that time. Examples of relevant potential changes that could impact our capital resources include:

 

   

the costs associated with our drug research and development activities, and additional costs we may incur if our development programs are delayed or are more expensive to implement than we currently anticipate;

 

   

changes in existing collaborative relationships, including the funding we receive in connection with those relationships;

 

   

the progress of our milestone and royalty producing activities;

 

   

acquisitions of other businesses or technologies;

 

   

the termination of our lease agreements;

 

   

the purchase of additional capital equipment;

 

   

cash payments or refunds we may be required to make pursuant to certain agreements with third parties;

 

   

competing technological and market developments; and

 

   

the cost of filing, prosecuting, defending and enforcing patent claims and other intellectual property rights, and the outcome of related litigation.

Additional capital may not be available on favorable terms, or at all. If additional capital is not available, we may be required to curtail operations significantly or to obtain funds by entering into arrangements with partners or other third parties that may require us to relinquish rights to certain of our technologies, products or potential markets that we would not otherwise relinquish.

 

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If, as the result of a merger, or otherwise, our collaborative partners were to change their strategy or the focus of their development and commercialization efforts with respect to our alliance products, the success of our alliance products could be adversely affected.

Our collaborative partners may change the focus of their development and commercialization efforts as the result of a merger. Pharmaceutical and biotechnology companies have historically re-evaluated their priorities from time to time, including following mergers and consolidations which are common in these industries, and two of our collaborative partners have recently entered into merger agreements. In January 2009, Wyeth, a collaborative partner of ours, and Pfizer announced that they have entered into a definitive merger agreement under which Pfizer will acquire Wyeth in a cash and stock transaction. Furthermore, in March 2009, Schering-Plough Corporation, another of our collaborative partners, and Merck & Co., Inc., or Merck, announced that their boards of directors have unanimously approved a definitive merger agreement pursuant to which Merck and Schering-Plough will combine, under the name Merck, in a stock and cash transaction. As a result of the consummation of these mergers our collaborative partners may develop and commercialize, either alone or with others, products and services that are similar to or competitive with our alliance products. Furthermore, the ability of our alliance products to reach their potential could be limited if our collaborative partners reduce or fail to increase spending related to such products as a result of these mergers.

If our collaborative partners terminate their collaborations with us or do not commit sufficient resources to the development, manufacture, marketing or distribution of our alliance products, we could be required to devote additional resources to our alliance products, seek new collaborative partners or abandon such alliance products, all of which could have an adverse effect on our business.

Third party intellectual property may prevent us or our partners from developing our potential products and we may owe a portion of any payments we receive from our collaborative partners to one or more third parties.

Our success will depend on our ability and the ability of our collaborative partners to avoid infringing the proprietary rights of others, both in the United States and in foreign countries. In addition, disputes with licensors under our license agreements may arise which could result in additional financial liability or loss of important technology and potential products and related revenue, if any. Further, the manufacture, use or sale of our potential products or our collaborative partners’ products or potential products may infringe the patent rights of others. This could impact AVINZA, PROMACTA, bazedoxifene, lasofoxifene, LGD-4665, PS433540, PS178990 and any other products or potential products.

Several drug companies and research and academic institutions have developed technologies, filed patent applications or received patents for technologies that may be related to our business. Others have filed patent applications and received patents that conflict with patents or patent applications we have licensed for our use, either by claiming the same methods or compounds or by claiming methods or compounds that could dominate those licensed to us. In addition, we may not be aware of all patents or patent applications that may impact our ability to make, use or sell any of our potential products. For example, US patent applications may be kept confidential while pending in the United States Patent and Trademark Office and patent applications filed in foreign countries are often first published six months or more after filing.

On March 4, 2008, Rockefeller filed suit in the United States District Court for the Southern District of New York, against us alleging, among other things, a breach by us of our September 30, 1992 license agreement with Rockefeller, as well as other causes of action for unjust enrichment, quantum meruit, specific performance to perform an audit and declaratory relief. In February 2009 we reached a settlement with Rockefeller whereby the parties resolved all disputes that have arisen between them, including Rockefeller’s primary claim relating to the development of PROMACTA as well our counterclaims. See “Item 3. Legal Proceedings.”

Other possible disagreements or litigation with our collaborative partners could delay our ability and the ability of our collaborative partners to achieve milestones or our receipt of other payments. In addition, other

 

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possible disagreements or litigation could delay, interrupt or terminate the research, development and commercialization of certain potential products being developed by either our collaborative partners or by us. The occurrence of any of the foregoing problems could be time-consuming and expensive and could adversely affect our business.

Third parties have not directly threatened an action or claim against us, although we do periodically receive other communications or have other conversations with the owners of other patents or other intellectual property. If others obtain patents with conflicting claims, we may be required to obtain licenses to those patents or to develop or obtain alternative technology. We may not be able to obtain any such licenses on acceptable terms, or at all. Any failure to obtain such licenses could delay or prevent us from pursuing the development or commercialization of our potential products.

In general, litigation claims can be expensive and time consuming to bring or defend against and could result in settlements or damages that could significantly impact our results of operations and financial condition. We cannot predict or determine the outcome of these matters or reasonably estimate the amount or range of amounts of any fines or penalties that might result from a settlement or an adverse outcome. However, a settlement or an adverse outcome could have a material adverse effect on our financial position, liquidity and results of operations.

We may not be able to hire and/or retain key employees.

If we are unable to hire and/or retain key employees, we may not have sufficient resources to successfully manage our assets or our business, and we may not be able to perform our obligations under various contracts and commitments. Furthermore, there can be no assurance that we will be able to retain all of Pharmacopeia’s key management and scientific personnel. If we fail to retain such key employees, we may not realize the anticipated benefits of the merger. Either of these could have substantial negative impacts on our business and our stock price.

Our stock price has been volatile and could experience a sudden decline in value.

Our common stock has experienced significant price and volume fluctuations and may continue to experience volatility in the future. As a result, you may not be able to sell your shares quickly or at the latest market price if trading in our stock is not active or the volume is low. Many factors may have a significant impact on the market price of our common stock, including, but not limited to, the following factors: results of or delays in our preclinical studies and clinical trials; the success of our collaboration agreements; publicity regarding actual or potential medical results relating to products under development by us or others; announcements of technological innovations or new commercial products by us or others; developments in patent or other proprietary rights by us or others; comments or opinions by securities analysts or major stockholders; future sales of our common stock by existing stockholders; regulatory developments or changes in regulatory guidance; litigation or threats of litigation; economic and other external factors or other disaster or crises; the departure of any of our officers, directors or key employees; period-to-period fluctuations in financial results; and limited daily trading volume.

The Financial Industry Regulatory Authority, or FINRA, (formerly the National Association of Securities Dealers, Inc.) and the Securities and Exchange Commission, or SEC, have adopted certain new rules. If we were unable to continue to comply with the new rules, we could be delisted from trading on the NASDAQ Global Market, or Nasdaq, and thereafter trading in our common stock, if any, would be conducted through the over-the-counter market or on the Electronic Bulletin Board of FINRA. As a consequence of such delisting, an investor would likely find it more difficult to dispose of, or to obtain quotations as to the price of, our common stock. Delisting of our common stock could also result in lower prices per share of our common stock than would otherwise prevail.

 

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We may not be successful in entering into additional out-license agreements on favorable terms, which may adversely affect our liquidity or require us to alter development plans on our products.

We have entered into several out-licensing agreements for the development and commercialization of our products. Although we expend considerable resources on internal research and development for our proprietary programs, we may not be successful in entering into additional out-licensing agreements under favorable terms due to several factors including:

 

   

the difficulty in creating valuable product candidates that target large market opportunities;

 

   

research and spending priorities of potential licensing partners;

 

   

willingness of and the resources available to pharmaceutical and biotechnology companies to in-license product candidates for their clinical pipelines; or

 

   

differences of opinion with potential partners on the valuation of products we are seeking to out-license.

The inability to enter into out-licensing agreements under favorable terms and to earn milestone payments, license fees and/or upfront fees may adversely affect our liquidity and may force us to curtail or delay development of some or all of our proprietary programs, which in turn may harm our business and the value of our stock.

Our product development involves a number of uncertainties, and we may never generate sufficient collaborative payments and royalties from the development of products to become profitable.

We were founded in 1987. We have incurred significant losses since our inception. As of December 31, 2008, our accumulated deficit was $679.6 million.

Most of our products in development will require extensive additional development, including preclinical testing and human studies, as well as regulatory approvals, before they can be marketed. We cannot predict if or when any of the products we are developing or those being developed with our partners will be approved for marketing. There are many reasons why we or our collaborative partners may fail in our efforts to develop our potential products, including the possibility that: preclinical testing or human studies may show that our potential products are ineffective or cause harmful side effects; the products may fail to receive necessary regulatory approvals from the FDA or foreign authorities in a timely manner, or at all; the products, if approved, may not be produced in commercial quantities or at reasonable costs; the products, if approved, may not achieve commercial acceptance; regulatory or governmental authorities may apply restrictions to our products, which could adversely affect their commercial success; or the proprietary rights of other parties may prevent us or our partners from marketing the products.

Any product development failures for these or other reasons, whether with our products or our partners’ products, may reduce our expected revenues, profits, and stock price.

The past restatement of our consolidated financial statements increased the possibility of legal or administrative proceedings. Any future material weaknesses or deficiencies in our internal control over financial reporting could harm stockholder and business confidence on our financial reporting, our ability to obtain financing and other aspects of our business.

We determined that our consolidated financial statements for the years ended December 31, 2002 and 2003, and for the first three quarters of 2004, as described in more detail in our 2004 Annual Report on Form 10-K, should be restated. As a result of the restatement, we have become subject to a number of additional risks and uncertainties. We expect to continue to incur unanticipated accounting and legal costs as noted below. In addition, the SEC has instituted a formal investigation into our restated consolidated financial statements

 

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identified above. This investigation will likely continue to divert more of our management’s time and attention and cause us to continue to incur substantial costs. Such investigations can also lead to fines or injunctions or orders with respect to future activities, as well as further substantial costs and diversion of management time and attention.

While no material weaknesses were identified as of December 31, 2008, we cannot assure you that material weaknesses will not be identified in future periods. The existence of one or more material weakness or significant deficiency could result in errors in our consolidated financial statements. Substantial costs and resources may be required to rectify any internal control deficiencies. If we fail to achieve and maintain the adequacy of our internal controls in accordance with applicable standards, we may be unable to conclude on an ongoing basis that we have effective internal controls over financial reporting. If we cannot produce reliable financial reports, our business and financial condition could be harmed, investors could lose confidence in our reported financial information, or the market price of our stock could decline significantly. In addition, our ability to obtain additional financing to operate and expand our business, or obtain additional financing on favorable terms, could be materially and adversely affected, which, in turn, could materially and adversely affect our business, our financial condition and the market value of our securities. Moreover, our reputation with customers, lenders, investors, securities analysts and others may be adversely affected.

Challenges to or failure to secure patents and other proprietary rights may significantly hurt our business.

Our success will depend on our ability and the ability of our licensors to obtain and maintain patents and proprietary rights for our potential products both in the United States and in foreign countries. Patents may not be issued from any of these applications currently on file, or, if issued, may not provide sufficient protection. Our patent position, like that of many biotechnology and pharmaceutical companies, is uncertain and involves complex legal and technical questions for which important legal principles are unresolved. We may not develop or obtain rights to products or processes that are patentable. Even if we do obtain patents, such patents may not adequately protect the technology we own or have licensed. In addition, others may challenge, seek to invalidate, infringe or circumvent any patents we own or license and rights we receive under those patents may not provide competitive advantages to us.

Any conflicts resulting from the patent rights of others could significantly reduce the coverage of our patents and limit our ability to obtain meaningful patent protection. We have had and will continue to have discussions with our current and potential collaborative partners regarding the scope and validity of our patents and other proprietary rights. If a collaborative partner or other party successfully establishes that our patent rights are invalid, we may not be able to continue our existing collaborations beyond their expiration. Any determination that our patent rights are invalid also could encourage our collaborative partners to seek early termination of our agreements. Such invalidation could adversely affect our ability to enter into new collaborations.

We may also need to initiate litigation, which could be time-consuming and expensive, to enforce our proprietary rights or to determine the scope and validity of others’ rights. If litigation occurs, a court may find our patents or those of our licensors invalid or may find that we have infringed on a competitor’s rights. In addition, if any of our competitors have filed patent applications in the United States which claim technology we also have invented, the United States Patent and Trademark Office may require us to participate in expensive interference proceedings to determine who has the right to a patent for the technology.

We also rely on unpatented trade secrets and know-how to protect and maintain our competitive position. We require our employees, consultants, collaborative partners and others to sign confidentiality agreements when they begin their relationship with us. These agreements may be breached, and we may not have adequate remedies for any breach. In addition, our competitors may independently discover our trade secrets.

 

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We will have continuing obligations to indemnify the buyers of our commercial product lines, and may be subject to other liabilities related to the sale of our commercial product lines.

In connection with the sale of our AVINZA product line, we have agreed to indemnify King in certain cases for a period of 30 months after the closing of the sale of the AVINZA product line in February 2007, including any breach of certain representations, warranties or covenants contained in the asset purchase agreement. In addition, we have agreed to indemnify Eisai, the purchaser of our Oncology product line, for damages suffered by Eisai arising from any breach of our representations, warranties, covenants or obligations in the asset purchase agreement. Our obligation to indemnify Eisai extends beyond the closing of the sale of our Oncology product line in October 2006 up to, in some cases, 36 months and, in other cases, until the expiration of the applicable statute of limitations. In a few instances, our obligation to indemnify Eisai survives in perpetuity.

Under certain circumstances, the asset purchase agreement for the AVINZA product line also allows King to set off indemnification claims against the royalty payments payable to us, including AVINZA royalty payments. Under the asset purchase agreements, our exposure for any indemnification claim brought by King or Eisai is limited to $40.0 million and $30.0 million, respectively. However, in certain matters, our indemnification obligation is not subject to the foregoing limits on liability. For example, we are obligated to indemnify King, without limitation, for all liabilities arising under certain agreements with Catalent Pharma Solutions related to the manufacture of AVINZA. Similarly, we are obligated to indemnify Eisai, without limitation, for all liabilities related to certain claims regarding promotional materials for the ONTAK and Targretin drug products. We cannot predict the liabilities that may arise as a result of these matters. Any claims related to our indemnification obligations to King or Eisai could materially and adversely affect our financial condition.

As previously disclosed, in connection with the AVINZA sale transaction, King assumed our obligation to make payments to Organon based on net sales of AVINZA (the fair value of which was $58.5 million as of December 31, 2008). As Organon did not consent to the legal assignment of the co-promote termination obligation from us to King, we remain liable to Organon in the event King defaults on this obligation. Any requirement to pay a material amount to Organon, could adversely affect our business and the price of our securities.

The sale of our commercial product lines also exposes us to product liability risks on products we sold prior to divesting these product lines. For example, such products may need to be recalled to address regulatory issues. A successful product liability claim or series of claims brought against us could result in payment of significant amounts of money and divert management’s attention from running our business.

We believe that we carry reasonably adequate insurance for product liability claims. However, we may not be able to maintain our insurance on commercially reasonable terms, or our insurance may not provide adequate protection in the case of a product liability claim. To the extent that product liability insurance, if available, does not cover potential claims, we will be required to self-insure the risks associated with such claims.

If our partners do not reach the market with our alliance products before our competitors offer products for the same or similar uses, or if our partners are not effective in marketing our alliance products, our revenues from product sales, if any, will be reduced.

We face intense competition in our development activities. Our competitors might succeed in obtaining regulatory approval for competitive products more rapidly than our partners can for our products. In addition, competitors might develop technologies and products that are less expensive and perceived to be safer or more effective than those being developed by us or our partners, which could impair our product development and render our technology obsolete.

 

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We use hazardous materials, which may expose us to significant liability.

In connection with our research and development activities, we handle hazardous materials, chemicals and various radioactive compounds. To properly dispose of these hazardous materials in compliance with environmental regulations, we are required to contract with third parties. We believe that we carry reasonably adequate insurance for toxic tort claims. However, we cannot eliminate the risk or predict the exposure of accidental contamination or injury from the handling and disposing of hazardous materials, whether by us or our third-party contractors. Any accident in the handling and disposing of hazardous materials may expose us to significant liability.

Our shareholder rights plan and charter documents may hinder or prevent change of control transactions.

Our shareholder rights plan and provisions contained in our certificate of incorporation and bylaws may discourage transactions involving an actual or potential change in our ownership. In addition, our Board of Directors may issue shares of preferred stock without any further action by the stockholders. Such restrictions and issuances may have the effect of delaying or preventing a change in our ownership. If changes in our ownership are discouraged, delayed or prevented, it would be more difficult for our current Board of Directors to be removed and replaced, even if you or our other stockholders believe that such actions are in the best interests of us and our stockholders.

We may lose some or all of the value of some of our short term investments.

We engage one or more third parties to manage some of our cash consistent with an investment policy that allows a range of investments and maturities. The investments are intended to maintain safety of principal while providing liquidity adequate to meet projected cash requirements. Risks of principal loss are to be minimized through diversified short and medium term investments of high quality, but the investments are not in every case guaranteed or fully insured. As a result of changes in the credit market, one of our short term investments in commercial paper is in default. We intend to pursue collection efforts, but we might not recoup some or all of our investment in the commercial paper. In addition, from time to time we may suffer other losses on our short term investment portfolio.

We may require additional money to run our business and may be required to raise this money on terms which are not favorable to us or which reduce our stock price.

We may need to complete additional equity or debt financings to fund our operations. Our inability to obtain additional financing could adversely affect our business. Financings may not be available at all or on terms favorable to us. In addition, these financings, if completed, may not meet our capital needs and could result in substantial dilution to our stockholders.

If adequate funds are not available, we may be required to delay, reduce the scope of or eliminate one or more of our research or drug development programs. We may also be required to liquidate our business or file for bankruptcy protection. Alternatively, we may be forced to attempt to continue development by entering into arrangements with collaborative partners or others that require us to relinquish some or all of our rights to technologies or drug candidates that we would not otherwise relinquish.

Our drug development programs will require substantial additional future funding which could hurt our operational and financial condition.

Our drug development programs require substantial additional capital to successfully complete them, arising from costs to: conduct research, preclinical testing and human studies; establish pilot scale and commercial scale manufacturing processes and facilities; and establish and develop quality control, regulatory, marketing, sales and administrative capabilities to support these programs.

 

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Our future operating and capital needs will depend on many factors, including: the pace of scientific progress in our research and development programs and the magnitude of these programs; the scope and results of preclinical testing and human studies; the time and costs involved in obtaining regulatory approvals; the time and costs involved in preparing, filing, prosecuting, maintaining and enforcing patent claims; competing technological and market developments; our ability to establish additional collaborations; changes in our existing collaborations; the cost of manufacturing scale-up; and the effectiveness of our commercialization activities.

We expect our research and development expenditures over the next three years to continue to be significant. However, we base our outlook regarding the need for funds on many uncertain variables. Such uncertainties include regulatory approvals, the timing of events outside our direct control such as product launches by partners and the success of such product launches, negotiations with potential strategic partners, possible sale of assets or other transactions and other factors. Any of these uncertain events can significantly change our cash requirements.

While we expect to fund our research and development activities from cash generated from AVINZA and PROMACTA royalties and royalties and milestones from our partners in various past and future collaborations to the extent possible, if we are unable to do so, we may need to complete additional equity or debt financings or seek other external means of financing. These financings could depress our stock price. If additional funds are required to support our operations and we are unable to obtain them on terms favorable to us, we may be required to cease or reduce further development or commercialization of our products, to sell some or all of our technology or assets or to merge with another entity.

Significant returns of products we sold prior to selling our commercial businesses could harm our operating results.

Under our agreements to sell our commercial businesses, we remain financially responsible for returns of our products sold before those businesses were transferred to their respective buyers. Consequently, if returns of those products are higher than expected, we could incur substantial expenses for processing and issuing refunds for those returns which, in turn, could negatively impact our financial results. The amount of returns could be affected by a number of factors including, but not limited to, ongoing product demand, product rotation at distributors and wholesalers, and product stability issues.

Our results of operations and liquidity needs could be materially negatively affected by market fluctuations and economic downturn.

Our results of operations could be materially negatively affected by economic conditions generally, both in the U.S. and elsewhere around the world. Continuing concerns over inflation, energy costs, geopolitical issues, the availability and cost of credit, the U.S. mortgage market and a declining residential real estate market in the U.S. have contributed to increased volatility and diminished expectations for the economy and the markets going forward. These factors, combined with volatile oil prices, declining business and consumer confidence and increased unemployment, have precipitated an economic recession and fears of a possible depression. Domestic and international equity markets continue to experience heightened volatility and turmoil. These events and the continuing market upheavals may have an adverse effect on us. In the event of a continuing market downturn, our results of operations could be adversely affected by those factors in many ways, including making it more difficult for us to raise funds if necessary, and our stock price may further decline.

Our investment securities consist primarily of money market funds, corporate debt obligations and U.S. government agency securities. We do not have any auction rate securities. Recently, there has been concern in the credit markets regarding the value of a variety of mortgage-backed securities and the resultant effects on various securities markets. We cannot provide assurance that our investments are not subject to adverse changes in market value. If our investments experience adverse changes in market value, we may have less capital to fund our operations.

 

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We may be unable to successfully integrate the business of Pharmacopeia and realize the anticipated benefits of the merger.

In December 2008, we completed our merger with Pharmacopeia. The success of the merger will depend, in part, on our ability to realize the anticipated synergies, growth opportunities and cost savings from integrating Pharmacopeia’s business with our business. Our success in realizing these benefits and the timing of this realization depend upon the successful integration of the operations of Pharmacopeia. The integration of two independent companies is a complex, costly and time-consuming process. It is possible that the integration process could result in the loss of key employees, diversion of each company’s management’s attention, the disruption or interruption of, or the loss of momentum in, each company’s ongoing business or inconsistencies in standards, controls, procedures and policies, any of which could adversely affect either company’s ability to maintain relationships with licensors, collaborators, partners, suppliers and employees or our ability to achieve the anticipated benefits of the merger, or could reduce our earnings or otherwise adversely affect the business and financial results of the combined company and, as a result, adversely affect the market price of our common stock.

We expect to incur significant costs and commit significant management time integrating Pharmacopeia’s business operations, technology, development programs, products and personnel with those of ours. If we do not successfully integrate the business of Pharmacopeia, the expenditure of these costs will reduce our cash position.

Impairment charges pertaining to goodwill, identifiable intangible assets or other long-lived assets from the merger with Pharmacopeia could have an adverse impact on our results of operations and the market value of our common stock.

The total purchase price pertaining to our merger with Pharmacopeia has been allocated to Pharmacopeia’s net tangible assets, identifiable intangible assets, in process research and development and goodwill. To the extent the value of goodwill or identifiable intangible assets or other long-lived assets become impaired, we will be required to incur material charges relating to the impairment. Any impairment charges could have a material adverse impact on our results of operations and the market value of our common stock.

We may undertake strategic acquisitions in the future and any difficulties from integrating such acquisitions could adversely affect our stock price, operating results and results of operations.

We may acquire companies, businesses and products that complement or augment our existing business. We may not be able to integrate any acquired business successfully or operate any acquired business profitably. Integrating any newly acquired business could be expensive and time-consuming. Integration efforts often take a significant amount of time, place a significant strain on managerial, operational and financial resources and could prove to be more difficult or expensive than we predict. The diversion of our management’s attention and any delay or difficulties encountered in connection with any future acquisitions we may consummate could result in the disruption of our on-going business or inconsistencies in standards and controls that could negatively affect our ability to maintain third-party relationships. Moreover, we may need to raise additional funds through public or private debt or equity financing, or issue additional shares, to acquire any businesses or products, which may result in dilution for stockholders or the incurrence of indebtedness.

As part of our efforts to acquire companies, business or product candidates or to enter into other significant transactions, we conduct business, legal and financial due diligence with the goal of identifying and evaluating material risks involved in the transaction. Despite our efforts, we ultimately may be unsuccessful in ascertaining or evaluating all such risks and, as a result, might not realize the intended advantages of the transaction. If we fail to realize the expected benefits from acquisitions we may consummate in the future, whether as a result of unidentified risks, integration difficulties, regulatory setbacks and other events, our business, results of operations and financial condition could be adversely affected. If we acquire product candidates, we will also need to make certain assumptions about, among other things, development costs, the likelihood of receiving regulatory approval and the market for such product candidates. Our assumptions may prove to be incorrect, which could cause us to fail to realize the anticipated benefits of these transactions.

 

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In addition, we will likely experience significant charges to earnings in connection with our efforts, if any, to consummate acquisitions. For transactions that are ultimately not consummated, these charges may include fees and expenses for investment bankers, attorneys, accountants and other advisors in connection with our efforts. Even if our efforts are successful, we may incur, as part of a transaction, substantial charges for closure costs associated with elimination of duplicate operations and facilities and acquired in-process research and development charges. In either case, the incurrence of these charges could adversely affect our results of operations for particular quarterly or annual periods.

The drug research and development industry is highly competitive and subject to technological change, and we may not have the resources necessary to compete successfully.

Many of our competitors have access to greater financial, technical, research, marketing, sales, distribution, service and other resources than we do. Moreover, the pharmaceutical and biotechnology industries are characterized by continuous technological innovation. We anticipate that we will face increased competition in the future as new companies enter the market and our competitors make advanced technologies available. Technological advances or entirely different approaches that we or one or more of our competitors develop may render our products, services and expertise obsolete or uneconomical. Additionally, the existing approaches of our competitors or new approaches or technologies that our competitors develop may be more effective than those we develop. We may not be able to compete successfully with existing or future competitors.

We have excess space available for sublease at our facilities and we may not be able to find qualified sublease tenants.

We have entered into long-term, non-cancellable real estate arrangements for space which, as a result of reductions in our workforce and our acquisition of Pharmacopeia, are considered to be in excess of our current requirements. We currently have a tenant who is subleasing one of our facilities and we are actively looking for additional sublease tenants to sublease up to approximately 80,000 square feet of vacant space or space that could be made available through changes in the current layout of our operations. We will continue to be responsible for all carrying costs of these facilities until such time as we can sublease these facilities or terminate the applicable leases based on the contractual terms of the lease agreements. However, the commercial real estate market conditions in the United States have resulted in a surplus of business facilities making it difficult to sublease properties. If we are unable to find additional sublease tenants we may not meet our expected estimated levels of sublease income or we may be required to terminate these leases at a substantial cost, and, accordingly, our results of operations could be materially and adversely affected.

 

Item 1B. Unresolved Staff Comments

None.

 

Item 2. Properties

We currently occupy an 82,500 square foot office and laboratory facility in San Diego, California leased through November 2021, which is a building we previously owned and sold and leased back on November 9, 2006. We lease approximately 99,000 square feet in three facilities in Cranbury, New Jersey under leases that expire in 2016. We believe these facilities are adequate to meet our space requirements for the foreseeable future.

We also lease a 52,800 square foot facility in San Diego that is leased through July 2015. In January 2008, we began subleasing the 52,800 square foot facility under a sublease through July 2015. We fully vacated this facility in February 2008.

 

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Item 3. Legal Proceedings

SEC Investigation

The SEC issued a formal order of private investigation dated September 7, 2005, to investigate the circumstances surrounding restatement of our consolidated financial statements for the years ended December 31, 2002 and 2003, and for the first three quarters of 2004. The SEC’s investigation is ongoing and we are cooperating with the investigation.

Other Matters

We and Seragen, Inc., our subsidiary, were named parties to Sergio M. Oliver, et al. v. Boston University, et al. , a shareholder class action filed on December 17, 1998 in the Court of Chancery in the State of Delaware. We and Seragen were dismissed from the action, but such dismissal is subject to appeal and we and Seragen may have possible indemnification obligations with respect to certain defendants. As of December 31, 2008, we have not accrued an indemnification obligation based on our assessment that our responsibility for any such obligation is not probable or estimable.

On March 4, 2008, Rockefeller filed suit in the United States District Court for the Southern District of New York, against us alleging, among other things, a breach by us of our September 30, 1992 license agreement with Rockefeller, as well as other causes of action for unjust enrichment, quantum meruit, specific performance to perform an audit and declaratory relief. In February 2009, we reached a settlement with Rockefeller whereby the parties resolved all disputes that have arisen between them, including Rockefeller’s primary claim relating to the development of PROMACTA as well our counterclaims. As part of the settlement, the parties executed mutual releases and agreed to jointly seek dismissal with prejudice of all claims, demands and causes of action, whether known or unknown, arising out of or based upon the license agreement, the ongoing litigation, PROMACTA, LGD-4665, and any other compound developed by us that was subject to the license agreement. We also agreed to pay Rockefeller, $5.0 million immediately upon settlement, $1.0 million on or before February 10, 2010, $1.0 million on or before February 10, 2011, and 50% of any milestone payment and 5.88% to 7.0% of certain royalties, in each case received by us pursuant to an agreement with SmithKline Beecham Corporation (now known as GlaxoSmithKline) entered into on December 29, 1994. We also agreed to pay Rockefeller 1.5% of world-wide net sales of LGD-4665 as certain payments are received by us pursuant to our agreement with SmithKline Beecham Corporation entered into on December 17, 2008. As of December 31, 2008, we have recorded a liability of $7.0 million related to the settlement.

On October 10, 2008, we received notice that a putative class action complaint was filed in the Superior Court of New Jersey, Mercer County (Equity Division) by Allen Heilman, one of Phamacopeia’s stockholders, against Pharmacopeia, the members of its Board of Directors, us and two of our wholly owned subsidiaries. The complaint generally alleges that Pharmacopeia’s Board of Directors’ decision to enter into the proposed transaction with us on the terms contained in the proposed merger agreement constitutes a breach of fiduciary duty and gives rise to other unspecified state law claims. The complaint also alleges that we and two of our wholly owned subsidiaries aided and abetted Pharmacopeia’s Board of Directors’ breach of fiduciary duty. In addition, the complaint alleges that the named plaintiff will seek “equitable relief,” including among other things, an order preliminarily and permanently enjoining the proposed transaction. While we believe that neither Ligand nor Pharmacopeia engaged in any wrongful acts, in an effort to minimize the cost and expense of any litigation, in December 2008, we entered into a memorandum of understanding, or MOU, with the named plaintiff providing for the settlement of the lawsuit. Subject to court approval and further definitive documentation, the MOU provides a release and settlement by the purported class of all claims against Pharmacopeia, us, and our affiliates and agents in connection with the complaint. Pursuant to the MOU we have agreed not to oppose any fee application by plaintiffs’ counsel that does not exceed $0.2 million, which has been recorded as a liability at December 31, 2008.

 

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In addition, from time to time we are subject to various lawsuits and claims with respect to matters arising out of the normal course of our business. Due to the uncertainty of the ultimate outcome of these matters, the impact on future financial results is not subject to reasonable estimates.

 

Item 4. Submission of Matters to a Vote of Security Holders

There were no matters submitted to a vote of security holders in the fourth quarter ended December 31, 2008.

Executive Officers of the Registrant

The names of the executive officers of the Company and their ages, titles and biographies as of March 1, 2008 are set forth below.

John L. Higgins, 38, joined the Company in January 2007 as President and Chief Executive Officer and he was also appointed to the Board in March 2007. Prior to joining the Company, Mr. Higgins served as Chief Financial Officer at Connetics Corporation, a specialty pharmaceutical company, since 1997, and also served as Executive Vice President, Finance and Administration and Corporate Development at Connetics since January 2002 until its acquisition by Stiefel Laboratories, Inc. in December 2006. Before joining Connetics, he was a member of the executive management team at BioCryst Pharmaceuticals, Inc., a biopharmaceutical company. Currently, he is a Director of BioCryst and serves as Chairperson of its Audit Committee. Before joining BioCryst in 1994, Mr. Higgins was a member of the healthcare banking team of Dillon, Read & Co. Inc., an investment banking firm. Mr. Higgins serves as chairman of CoMentis, Inc, a biopharmaceutical company, and has served as a director of numerous public and private companies. He received his A.B. from Colgate University, graduating Magna Cum Laude.

Martin D. Meglasson, Ph.D ., 58, joined the Company in February 2004 as Vice President, Discovery Research. Prior to joining the Company, Dr. Meglasson was Director of Preclinical Pharmacology at Pharmacia, Inc. where he engaged in research and development of drugs for central nervous system and infectious diseases from 1998 to 2003. From 1996 to 1998, Dr. Meglasson served as Director of Endocrine and Metabolic Research, engaged in diabetes and obesity research, and was a member of the Exploratory Development Committee at Pharmacia & Upjohn. From 1988 to 1996, he was a researcher in the fields of diabetes and obesity at The Upjohn Co. Dr. Meglasson has participated in the discovery and development of two marketed drugs, is an inventor of 18 U.S. patents, and author of 70 scientific publications. Dr. Meglasson received his Ph.D. in pharmacology from the University of Houston and post-doctoral training at the University of Pennsylvania School of Medicine.

Zofia E. Dziewanowska, M.D., Ph.D. , 67, has served as our Vice President, Clinical Research and Regulatory since February 2008. Dr. Dziewanowska joined the Company in April 2002 and previously served as the Vice President in charge of the Clinical Research Department, responsible for evaluation of all drugs. Her work in the industry began as an Associate Director of International Clinical Pharmacology at Merck Company, N.J. and subsequently at Hoffmann-La Roche Inc., the last few years until 1994 as Vice President and the Head of Clinical Research and Development for the United States. Since 1994, she held successive positions as Senior Vice President of Global Clinical Research and Development at Genta, Inc, Cypros Pharma and MAXIA, Inc. Dr. Dziewanowska also served as Vice Chair of a Medical Section Steering Committee for PhRMA. She has also served as Chair of an International Sub-committee and a Chair of Education Committee for physicians in Pharmaceutical Medicine at AAPP. Dr. Dziewanowska obtained her M.D. from the Medical School University of Warsaw and Ph.D. from the Polish Academy of Science. Academic affiliations include faculty membership at The Medical School of Cornell University, Rockefeller University, and The Medical School of the University of London. Her name is listed in several current Marquis’ “Who is Who”.

Syed Kazmi, Ph.D., MBA, 51, has served as our Vice President, Business Development & Strategic Planning since July 2007. Dr. Kazmi has more than 18 years of Pharmaceutical R&D and Business development

 

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experience. From 1995 until June 2007, he held various positions at Ligand, including Senior Scientist in Molecular Endocrinology, Director of Project Management and leader of multiple drug development teams, and Senior Director of Business Development. Prior to joining Ligand, Dr. Kazmi worked in discovery research at Johnson & Johnson from 1988 to 1995, where his most recent position was Principal Scientist in endocrinology and inflammation drug development programs. From 1985 to 1988, he held his postdoctoral research positions at McMaster University, Hamilton. Dr. Kazmi received a Ph.D. in biochemistry from J.N. University, New Delhi, and an executive MBA from San Diego State University.

John Sharp, CPA , 44, joined the Company in April 2007 as our Vice President, Finance and Chief Financial Officer. From November 2004 to April 2007, Mr. Sharp served as Vice President of Finance of Sequenom, Inc. and served as its Principal Accounting Officer since October 2005. From August 2000 to November 2004, Mr. Sharp served as Director of Accounting at Diversa Corporation, a publicly traded biotech company, where he was responsible for managing the overall accounting function, including financial reporting, internal controls, and corporate governance, during a period of significant company growth. From January 1994 until August 2000, Mr. Sharp was at the public accounting firm PricewaterhouseCoopers, most recently as a Senior Audit Manager. He received a B.S. from San Diego State University, and is a certified public accountant and a member of the Association of BioScience Financial Officers.

Charles S. Berkman, J.D. , 40, has served as our Vice President, General Counsel and Secretary since April 2007. Mr. Berkman joined the Company in November 2001 and previously served as Associate General Counsel and Chief Patent Counsel for the Company (and Secretary since March 2007). Prior to joining the Company, Mr. Berkman was an attorney at the international law firm of Baker & McKenzie from November 2000 to November 2001. Before that he served as an attorney at the law firm of Lyon & Lyon from 1993 to November 2000, where he specialized in intellectual property law. Mr. Berkman earned a BS in chemistry from the University of Texas and a JD from the University of Texas School of Law.

 

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PART II

 

Item 5. Market for Registrant’s Common Equity, Related Stockholder Matters, and Issuer Purchases of Equity Securities

Market Information

Our common stock is traded on the NASDAQ Global Market (formerly NASDAQ National Market) under the symbol “LGND”.

The following table sets forth the high and low intraday sales prices for our common stock on the NASDAQ Global Market and on the Pink Sheets, as applicable, for the periods indicated:

 

     Price Range
     High    Low

Year Ended December 31, 2008:

     

1st Quarter

   $ 5.00    $ 3.31

2nd Quarter

     4.55      2.16

3rd Quarter

     3.82      2.58

4th Quarter

     2.94      1.10

Year Ended December 31, 2007:

     

1st Quarter

   $ 13.03    $ 8.86

2nd Quarter

     10.30      6.37

3rd Quarter

     7.36      5.19

4th Quarter

     6.21      3.87

As of February 27, 2009, the closing price of our common stock on the NASDAQ Global Market was $2.71.

Holders

As of February 27, 2009, there were approximately 1,672 holders of record of the common stock.

Dividends

On March 22, 2007, we declared a cash dividend on our common stock of $2.50 per share. As we have an accumulated deficit, the dividend was recorded as a charge against additional paid-in capital. The aggregate amount of $252.7 million was paid on April 19, 2007 to shareholders of record as of April 5, 2007. We had previously never declared or paid any cash dividends on our capital stock. We do not intend to pay any additional cash dividends in the foreseeable future. We currently intend to retain future earnings, if any, to finance future growth.

 

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Performance Graph

The graph below shows the five-year cumulative total stockholder return assuming the investment of $100 and the reinvestment of dividends (a one-time dividend of $2.50 was declared on the common stock in April 2007) and is based on the returns of the component companies weighted monthly according to their market capitalizations. The graph compares total stockholder returns of the Company’s common stock, of all companies traded on the NASDAQ Stock market, as represented by the NASDAQ Composite ® Index, and of the NASDAQ Biotechnology Stock Index, as prepared by The NASDAQ Stock Market Inc. The NASDAQ Biotechnology Stock Index tracks approximately 168 domestic biotechnology stocks.

The stockholder return shown on the graph below is not necessarily indicative of future performance and the Company will not make or endorse any predictions as to future stockholder returns.

LOGO

 

     12/31/03     12/31/04     12/31/05     12/31/06     12/31/07     12/31/08  

Ligand

   100 %   79 %   76 %   75 %   44 %   24 %

NASDAQ Composite

   100 %   109 %   110 %   121 %   132 %   79 %

NASDAQ Biotechnology Stocks

   100 %   106 %   109 %   110 %   115 %   101 %

 

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Item 6. Selected Consolidated Financial Data

The following selected historical consolidated financial and other data are qualified by reference to, and should be read in conjunction with, our consolidated financial statements and the related notes thereto appearing elsewhere herein and “Management’s Discussion and Analysis of Financial Condition and Results of Operations.” Our selected statement of operations data set forth below for each of the years ended December 31, 2008, 2007, 2006, 2005, and 2004 and the balance sheet data as of December 31, 2008, 2007 2006, 2005, and 2004 are derived from our consolidated financial statements.

 

     Years Ended December 31,  
     2008     2007     2006 (2)     2005     2004  
     (in thousands, except share data)  

Consolidated Statement of Operations Data:

          

Royalties

   $ 20,305     $ 11,409     $ —       $ —       $ —    

Sale of royalty rights, net

     —         —         —         —         31,342  

Collaborative research and development and other revenues

     7,000       1,485       3,977       10,217       11,300  

Research and development expenses

     30,770       44,623       41,546       30,710       30,742  

General and administrative expenses

     23,785       30,410       43,908       23,134       12,580  

Write-off of acquired in-process research and development

     72,000       —         —         —         —    

Gain on sale leaseback

     1,964       1,964       3,397       —         —    

Loss from operations

     (97,276 )     (60,175 )     (78,080 )     (43,627 )     (680 )

Income (loss) from continuing operations

     (97,460 )     (34,759 )     (56,590 )     (36,035 )     2,684  

Discontinued operations (1)

     (654 )     316,447       24,847       (364 )     (47,825 )

Net income (loss)

     (98,114 )     281,688       (31,743 )     (36,399 )     (45,141 )

Basic per share amounts:

          

Income (loss) from continuing operations

   $ (1.02 )   $ (0.35 )   $ (0.70 )   $ (0.49 )   $ 0.04  

Discontinued operations (1)

     (0.01 )     3.22       0.31       —         (0.65 )
                                        

Net income (loss)

   $ (1.03 )   $ 2.87     $ (0.39 )   $ (0.49 )   $ (0.61 )
                                        

Weighted average number of common shares

     95,505,421       98,124,731       80,618,528       74,019,501       73,692,987  
                                        

Diluted per share amounts:

          

Income (loss) from continuing operations

   $ (1.02 )   $ (0.35 )   $ (0.70 )   $ (0.49 )   $ 0.03  

Discontinued operations (1)

     (0.01 )     3.22       0.31       —         (0.48 )
                                        

Net income (loss)

   $ (1.03 )   $ 2.87     $ (0.39 )   $ (0.49 )   $ (0.45 )
                                        

Weighted average number of common shares

     95,505,421       98,124,731       80,618,528       74,019,501       100,402,063  
                                        

 

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     December 31,  
     2008     2007     2006     2005     2004  
     (in thousands)  

Consolidated Balance Sheet Data:

          

Cash, cash equivalents, short-term
investments and restricted cash and investments

   $ 82,012     $ 95,819     $ 212,488     $ 88,756     $ 114,870  

Working capital (deficit) (3)

     23,315       58,975       64,747       (102,244 )     (48,505 )

Total assets

     171,448       173,278       326,053       314,619       332,466  

Current portion of deferred revenue, net

     10,301       —         57,981       157,519       152,528  

Current portion of deferred gain

     1,964       1,964       1,964       —         —    

Long-term obligations (excludes long-term portions of deferred revenue, net and deferred gain)

     58,743       53,048       85,780       173,280       174,214  

Long-term portion of deferred revenue, net

     16,819       2,546       2,546       4,202       4,512  

Long-term portion of deferred gain

     23,292       25,256       27,220       —         —    

Common stock subject to conditional redemption

     12,345       12,345       12,345       12,345       12,345  

Accumulated deficit

     (679,626 )     (581,512 )     (862,802 )     (831,059 )     (794,660 )

Total stockholders’ equity (deficit)

     (10,365 )     29,115       27,352       (110,419 )     (75,317 )

 

 

(1) We sold our Oncology Product Line (“Oncology”) on October 25, 2006 and our AVINZA Product Line (“AVINZA”) on February 26, 2007. The operating results for Oncology and AVINZA have been presented in our consolidated statements of operations as “Discontinued Operations.”
(2) Effective January 1, 2006, we adopted Statement of Financial Accounting Standards 123(R), Share-Based Payment , or SFAS 123(R), using the modified prospective transition method. The implementation of SFAS123(R) resulted in additional employee stock compensation expense of $4.8 million in 2006.
(3) Working capital (deficit) includes deferred product revenue recorded under the sell-through revenue recognition method.

 

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Item 7. Management’s Discussion and Analysis of Financial Condition and Results of Operations

Caution : This discussion and analysis may contain predictions, estimates and other forward-looking statements that involve a number of risks and uncertainties, including those discussed in Item 1A. “Risk Factors.” This outlook represents our current judgment on the future direction of our business. These statements include those related to our AVINZA royalty revenues, product returns, and product development. Actual events or results may differ materially from Ligand’s expectations. For example, there can be no assurance that our revenues or expenses will meet any expectations or follow any trend(s), that we will be able to retain our key employees or that we will be able to enter into any strategic partnerships or other transactions. We cannot assure you that we will receive expected AVINZA royalties to support our ongoing business or that our internal or partnered pipeline products will progress in their development, gain marketing approval or achieve success in the market. In addition, our ongoing SEC investigation, ongoing or future arbitration, or litigation or disputes with third parties may have a material adverse effect on us. Such risks and uncertainties, and others, could cause actual results to differ materially from any future performance suggested. We undertake no obligation to release publicly the results of any revisions to these forward-looking statements to reflect events or circumstances arising after the date of this annual report. This caution is made under the safe harbor provisions of Section 21E of the Securities Exchange Act of 1934, as amended.

Our trademarks, trade names and service marks referenced herein include Ligand. Each other trademark, trade name or service mark appearing in this annual report belongs to its owner.

References to “Ligand Pharmaceuticals Incorporated”, “Ligand”, the “Company”, “we” or “our” include our wholly owned subsidiaries—Ligand Pharmaceuticals International, Inc.; Seragen, Inc., or Seragen; Pharmacopeia, LLC; and Nexus Equity VI LLC, or Nexus.

Overview

We are a biotechnology company that focuses on drug discovering and early-stage development of pharmaceuticals that address critical unmet medical needs or that are more effective and/or safer than existing therapies, more convenient to administer and are cost effective. Our goal is to build a profitable company by generating income from research, milestone, and royalty revenues resulting from our collaborations with pharmaceutical partners.

On September 7, 2006, we announced the sale of ONTAK, Targretin capsules, Targretin gel, and Panretin gel to Eisai, Inc., or Eisai, and the sale of AVINZA to King Pharmaceuticals, Inc., or King. The Eisai sales transaction subsequently closed on October 25, 2006. The AVINZA sale transaction subsequently closed on February 26, 2007. Accordingly, the results for the Oncology and AVINZA Product Lines have been presented in our consolidated statements of operations as “Discontinued Operations.”

On December 23, 2008, we acquired all of the outstanding common shares of Pharmacopeia, Inc., or Pharmacopeia. As consideration, we issued 18.0 million shares of our common stock to Pharmacopeia stockholders, or 0.5985 shares for each outstanding Pharmacopeia share, as well as approximately $9.3 million in cash. Security holders of Pharmacopeia also received contingent value rights, under which they could receive an aggregate cash payment of $15.0 million under certain circumstances. Pharmacopeia was a clinical development stage biopharmaceutical company dedicated to discovering and developing novel small molecule therapeutics to address significant medical needs. Pharmacopeia’s strategy was to retain the rights to product candidates at least to clinical validation, and to continue development on its own New Drug Application, or NDA, filings and commercialization for selected indications. Pharmacopeia had a broad portfolio of clinical and preclinical candidates under development internally or by partners.

Our business strategy includes a targeted internal drug research and early-stage development capabilities. We believe that we have promising product candidates throughout our internal development programs. We also

 

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have research and development collaborations for our product candidates with numerous global pharmaceutical companies. We aim to create value for shareholders by advancing our internally developed programs through early clinical development and then entering licensing agreements with larger pharmaceutical and biotechnology companies with substantially greater development and commercialization infrastructure. In addition to advancing our R&D programs, we expect to collect licensing fees and royalties from existing and future license agreements. We aim to build a profitable company by generating income from our corporate licenses.

We currently receive royalty revenues from King Pharmaceuticals, or King, and GSK. In February 2007, we completed the sale of our AVINZA product line to King. As a result of the sale, we received the right to future royalties on the net sales of AVINZA through 2017. Through October 2008, we received a 15% royalty on AVINZA net sales. Subsequent royalty payments will be based upon calendar year net sales. If calendar year net sales are less than $200.0 million, the royalty payment will be 5% of all net sales. If calendar year net sales are greater than $200.0 million, the royalty payment will be 10% of all net sales less than $250.0 million, plus 15% of net sales greater than $250.0 million.

In December 2008, the U.S. Food and Drug Administration, or FDA, granted accelerated approval of GSK’s PROMACTA for the treatment of thrombocytopenia in patients with chronic immune (idiopathic) thrombocytopenic purpura, or ITP, who have had an insufficient response to corticosteroids, immunoglobulins or splenectomy. PROMACTA is the first oral thrombopoietin, or TPO, receptor agonist therapy for the treatment of adult patients with chronic ITP. As a result of the FDA’s approval of PROMACTA, we will be entitled to receive tiered royalties in the range of 5%-10% on annual net sales of PROMACTA. As part of a settlement agreement and mutual release we entered into on February 11, 2009 with The Rockefeller University, or Rockefeller, we agreed to pay a share of such royalties to Rockefeller. See “Item 3. Legal Proceedings”

We also have the potential to receive near-term royalties on product candidates resulting from our research and development collaboration arrangements with third party pharmaceutical companies if and when any such product candidate is ultimately approved by the FDA and successfully marketed. Our near-term product candidates are discussed below.

In addition to the accelerated approval granted for GSK’s PROMACTA for the treatment of thrombocytopenia in patients with chronic ITP, GSK also reported positive Phase II data in patients with thrombocytopenia associated with hepatitis C and initiated two Phase III trials in patients with hepatitis C in the fourth quarter of 2007 and a Phase III trial in patients with chronic liver disease (CLD) in early 2008. A Phase II study in patients with oncology-related thrombocytopenia is ongoing and a Phase I study is ongoing in patients with sarcoma receiving the adriamycin and ifosfamide regimen. In December 2008, GSK submitted a marketing authorization application in the EU and international for Revolade (Eltrombopag) for the treatment of thrombocytopenia in patients with chronic immune (idiopathic) thrombocytopenic purpura, or ITP.

Bazedoxifene (VIVIANT) is a product candidate that resulted from a collaboration with Wyeth. Bazedoxifene is a synthetic drug that was specifically designed to reduce the risk of osteoporotic fractures while at the same time protecting breast and uterine tissue. In June 2006, Wyeth submitted an NDA for bazedoxifene to the FDA for the prevention of postmenopausal osteoporosis. The FDA issued an approvable letter for bazedoxifene for this indication in April 2007. Wyeth received a second approvable letter in December 2007 and plans to have further discussions with the FDA to discuss the issues raised for the prevention indication. Wyeth also submitted a second NDA for bazedoxifene in the United States in July 2007 for the treatment of osteoporosis and an MAA to EMEA in September 2007 for the prevention and treatment of osteoporosis. Wyeth received a third approvable letter in the second quarter of 2008 for bazedoxifene for the treatment of osteoporosis. In the letter, the FDA requested information similar to that outlined in its approvable letter for bazedoxifene’s NDA for the prevention of postmenopausal osteoporosis issued in December 2007. This included further analyses concerning the incidence of stroke and venous thrombotic events. Wyeth indicated that it will file a complete response in 2009 and expects the FDA will convene an advisory committee to review the pending NDAs for both the treatment and prevention of postmenopausal osteoporosis with VIVIANT. In February 2009, VIVIANT

 

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received a positive Committee for Medicinal Products for Human Use (CHMP) opinion in Europe for the treatment of postmenopausal osteoporosis in women at increased risk of fracture.

Wyeth is also developing bazedoxifene in combination with PREMARIN (Aprela) as a progesterone-free treatment for menopausal symptoms. Two Phase III studies with bazedoxifene/conjugated estrogens (Aprela), showed reduced number and severity of hot flashes in symptomatic postmenopausal women by up to 80 percent, when compared with placebo. Wyeth expects to file an initial NDA no earlier than the first half of 2010.

We previously sold to Royalty Pharma AG, or Royalty Pharma, the rights to a total of 3.0% of net sales of bazedoxifene for a period of ten years following the first commercial sale of each product. After giving effect to the royalty sale, we will receive 0.5% of the first $400.0 million in net annual sales. If net annual sales are between $400.0 million and $1.0 billion, we will receive a net royalty of 1.5% on the portion of net sales between $400.0 million and $1.0 billion, and if annual sales exceed $1.0 billion, we will receive a net royalty of 2.5% on the portion of net sales exceeding $1.0 billion. Additionally, the royalty owed to Royalty Pharma may be reduced by one third if net product sales exceed certain thresholds across all indications.

Lasofoxifene (FABLYN) is a product candidate that resulted from our collaboration with Pfizer. In April 2007, Pfizer announced completion of the Postmenopausal Evaluation and Risk Reduction with lasofoxifene (PEARL) Phase III study with favorable efficacy and safety. Pfizer submitted an NDA and an MAA for osteoporosis treatment in December 2007 and January 2008, respectively. The FDA Advisory Committee in early September 2008 voted 9-3 in favor of approval of this drug and in January 2009, Pfizer received a complete response letter from the FDA requesting additional information for FABLYN. Pfizer is reviewing the letter and will work with the FDA to determine the appropriate next steps regarding its application. In December 2008 an EU Drug Panel granted a positive opinion for the approval of lasofoxifene in the EU for the treatment of osteoporosis in postmenopausal women at increased risk of fracture. Pfizer has also submitted NDA’s for osteoporosis prevention and vaginal atrophy, and the FDA issued non-approvable letters for both NDA’s.

Under the terms of our agreement with Pfizer, we are entitled to receive royalty payments equal to 6% of worldwide net sales of lasofoxifene for any indication. We previously sold to Royalty Pharma the rights to a total of 3% of net sales of lasofoxifene for a period of ten years following the first commercial sale of lasofoxifene. Accordingly, we will receive approximately 3% of worldwide net annual sales of lasofoxifene.

In December 2008, we entered into an exclusive, worldwide license agreement with SmithKline Beecham Corporation, doing business as GSK. Pursuant to the terms of the GSK agreement, we granted GSK the exclusive right to develop, manufacture and commercialize our LGD-4665 product candidate, as well as all other TPO-related molecules discovered by us. LGD-4665 is currently in a Phase II trial for treatment of thrombocytopenia, a condition of low-platelet levels commonly associated with a diverse range of clinical disorders. Under the terms of the GSK agreement, GSK paid us $5 million as an upfront license fee and agreed to pay us up to $158.0 million in development and commercial milestones and a royalty on net sales. In the first year of sales, royalties will be one-half of the regular royalty rate. GSK has the exclusive right to develop, manufacture and commercialize LGD-4665, as well as other TPO-related molecules discovered by us. GSK will direct all product development and commercialization and will be responsible for all costs going forward for development, patent maintenance and prosecution, and commercialization. We reported at the December 2008 American Society of Hematology annual meeting that LGD-4665 has the potential for weekly dosing, has differentiated clinical pharmacology from other products on the market and has promising potential efficacy in ITP, based on interim clinical study results.

Results of Operations

Total revenues for 2008 were $27.3 million, compared to $12.9 million in 2007 and $4.0 million in 2006. Our loss from continuing operations for 2008 was $97.5 million, or $1.02 per share, compared to $34.8 million, or $0.35 per share, in 2007 and $56.6 million, or $0.70 per share, in 2006.

 

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AVINZA Royalty Revenue

In connection with the sale of AVINZA, King is required to pay us a royalty on net sales of AVINZA. In accordance with the AVINZA purchase agreement, royalties are required to be reported and paid to us within 45 days of quarter-end during the 20 month period following the closing of the sale transaction (February 26, 2007). Thereafter, royalties will be paid on a calendar year basis. Such royalties are recognized in the quarter reported. Since there is a one quarter lag from when King recognizes AVINZA net sales to when King reports those sales and the corresponding royalties to us, we recognized AVINZA royalty revenues beginning in the second quarter of 2007. Royalty revenues were $20.3 million in 2008 and $11.4 million in 2007.

Collaborative Research and Development and Other Revenue

Collaborative research and development and other revenues for 2008 were $7.0 million compared to $1.5 million in 2007 and $4.0 million for 2006. Collaborative research and development and other revenues include reimbursement for ongoing research activities, earned milestones, and recognition of prior years’ up-front fees previously deferred in accordance with Staff Accounting Bulletin, or SAB No. 104— Revenue Recognition (SAB104). Revenue from distribution agreements includes recognition of up-front fees collected upon contract signing and deferred over the life of the distribution arrangement and milestones achieved under such agreements.

A comparison of collaborative research and development and other revenues is as follows (in thousands):

 

     Year Ended December 31,
     2008    2007    2006

Collaborative research and development

   $ —      $ —      $ 1,678

License fees

     5,000      —        —  

Milestones and other

     2,000      1,485      2,299
                    
   $ 7,000    $ 1,485    $ 3,977
                    

Collaborative Research and Development. The decrease in collaborative research and development revenue is due to the completion of the research phase of our collaborative arrangement with TAP, which concluded in June 2006.

License fees. During 2008, we received a $5.0 million up-front license fee as a result of entering into an agreement with GSK under which we have licensed worldwide exclusive rights to Ligand’s LGD-4665 product candidate and its other thrombopoietin (TPO)-related molecules to GSK.

Milestones and Other. Milestones in 2008 reflect $2.0 million received from GSK as a result of FDA approval of eltrombopag. Milestones in 2007 reflect $1.0 million received from GSK in connection with the filing of an NDA for eltrombopag and $0.5 million earned from Wyeth. Milestones in 2006 reflect $2.0 million received from GSK in connection with the commencement of Phase III studies of eltrombopag and $0.3 million received from Wyeth in connection with the filing of an NDA for Viviant (also known as bazedoxifene).

 

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Research and Development Expenses

Research and development expenses were $30.8 million in 2008 compared to $44.6 million in 2007 and $41.5 million in 2006. The major components of research and development expenses are as follows (in thousands):

 

     Years Ended December 31,
     2008    2007    2006

Research performed under collaboration agreements

   $ —      $ —      $ 1,968

Internal research programs

     21,626      21,954      22,110
                    

Total research

     21,626      21,954      24,078

Development costs

     9,144      22,669      17,468
                    

Total research and development

   $ 30,770    $ 44,623    $ 41,546
                    

Research and development expenses for 2007 included one-time severance benefits and stock compensation charges of $6.6 million incurred in connection with our restructuring and one-time stock compensation charges of $0.8 million incurred in connection with the equitable adjustment of stock options.

Spending for research expenses was $21.6 million for 2008 compared to $22.0 million for 2007. Research expenses for 2008 included $7.0 million related to a settlement agreement and mutual release we entered into with The Rockefeller University, or Rockefeller. Excluding the impact of the litigation settlement costs incurred in 2008 and one-time severance benefits and stock compensation charges incurred in connection with our restructuring and one-time stock compensation charges incurred in connection with the equitable adjustment of stock options incurred in 2007 , internal research program expenses decreased in 2008 when compared to 2007 due to lower headcount related expenses in connection with our restructuring and reduced outside service costs associated with our thrombopoietin (TPO) agonists program.

Spending for research expenses was $22.0 million for 2007 compared to $24.1 million for 2006. Excluding the impact of one-time severance benefits and stock compensation charges incurred in 2007, the decrease in internal research program expenses for 2007 compared to 2006 reflects reduced costs primarily due to lower headcount related expenses in connection with our restructuring.

Spending for development expenses decreased to $9.1 million for 2008 compared to $22.7 million for 2007. Excluding the impact of one-time severance benefits and stock compensation charges, expenses decreased for 2008 when compared to 2007 due to lower headcount related expenses in connection with our restructuring and reduced outside service costs associated with our thrombopoietin (TPO) agonists program.

Spending for development expenses increased to $22.7 million for 2007 compared to $17.5 million for 2006. Excluding the impact of one-time severance benefits and stock compensation charges, the increase primarily reflects increased spending on Phase I clinical trials for LGD-4665 TPO, which was our leading drug candidate.

 

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A summary of our significant internal research and development programs as of December 31, 2008 is as follows:

 

Program

  

Disease/Indication

  

Development Phase

Dual-Acting angiotensin and endothelin Receptor Antagonist (DARA)    Diabetic Nephropathy*    Phase II
Selective Androgen Receptor Modulators (SARMs) (agonists)   

Muscle wasting and frailty

   Pre-clinical
Chemokine Receptor (CCR1)    Inflammatory and autoimmune diseases    Pre-clinical
Small molecule Erythropoiein (EPO) receptor agonists    Chemotherapy-induced anemia and anemia due to kidney failure    Research
Selective Glucocorticoid Receptor Modulators (SGRMs)    Inflammation and cancer    Research
Androgen-independent Prostate Cancer (AiPC)    Prostate cancer    Research

 

* Phase II clinical trials conducted so far have studied patients with hypertension

We do not provide forward-looking estimates of costs and time to complete our ongoing research and development projects, as such estimates would involve a high degree of uncertainty. Uncertainties include our inability to predict the outcome of complex research, our inability to predict the results of clinical studies, regulatory requirements placed upon us by regulatory authorities such as the FDA and EMEA, our inability to predict the decisions of our collaborative partners, our ability to fund research and development programs, competition from other entities of which we may become aware of in future periods, predictions of market potential from products that may be derived from our research and development efforts, and our ability to recruit and retain personnel or third-party research organizations with the necessary knowledge and skills to perform certain research. Refer to “Item 1A. Risks Factors” for additional discussion of the uncertainties surrounding our research and development initiatives.

General and Administrative Expenses

General and administrative expenses were $23.8 million for 2008, compared to $30.4 million for 2007 and $43.9 million for 2006. General and administrative costs for 2008 were lower when compared to 2007 primarily due to lower headcount related expenses of $7.1 million (which included a one-time severance benefits $3.9 million in connection with our restructuring, and stock compensation charges of $1.0 million incurred in connection with the equitable adjustment of stock options), reduced outside consulting and audit fees of $3.6 million and reduced occupancy cost of $1.7 million. These reductions were partially offset by a $4.1 million charge for exit costs when we fully ceased use of one of our leased facilities in the first quarter of 2008 and increased legal expenses of $1.1 million primarily related to litigation with The Salk Institute for Biological Studies, or Salk, and Rockefeller.

The decrease for 2007 compared to 2006 is due to lower headcount in connection with our restructuring and reduced legal costs (as we incurred significant costs during 2006 in connection with the ongoing SEC investigation, shareholder litigation and our strategic initiative process) and consultant fees incurred in connection with our 2006 SOX compliance program. General and administrative expenses for 2007 include one-time severance benefits and stock compensation charges of $4.1 million incurred in connection with our restructuring and one-time stock compensation charges of $1.0 million incurred in connection with the equitable adjustment of stock options. General and administrative expenses for 2007 also include $2.1 million of legal and

 

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related costs incurred in connection with the ongoing SEC investigation of our financial statement restatement (See Part I, Item 3 “Legal Proceedings”).

Write-off of in-process research and development

For acquisitions prior to January 1, 2009, the fair value of acquired In-Process Research and Development (IPR&D) projects, which have no alternative future use and which have not reached technological feasibility at the date of acquisition were immediately expensed. We wrote-off $72.0 million of acquired in-process research and development related to the acquisition of Pharmacopeia, Inc. in 2008. The amount is related to internal and partnered product candidates targeting a variety of indications and currently in various stages of development ranging from preclinical to Phase II. Of the total amount, $29.0 million relates to product candidates currently in the preclinical stage of development, $9.0 million relates to product candidates currently in Phase I clinical trials and $34.0 million relates to product candidates currently in Phase II clinical trials.

We used the “income method” to determine the estimated fair values of acquired in-process research and development, which uses a discounted cash flow model and applies a probability weighting based on estimates of successful product development and commercialization to estimated future net cash flows resulting from projected revenues and related costs. These success rates take into account the stages of completion and the risks surrounding successful development and commercialization of the underlying product candidates. These cash flows were then discounted to present value using a discount rate of 40% for product candidates in the preclinical stage, 35% for product candidates currently in Phase I clinical trials and 30% for product candidates currently in Phase II clinical trials.

The above assumptions were used solely for the purposes of estimating fair values of these product candidates as of the date of their acquisition. However, we cannot provide assurance that the underlying assumptions used to forecast the cash flows or the timely and successful completion of development and commercialization will materialize, as estimated. Consequently, the eventual realized value of the acquired in-process research and development may vary from its estimated value at the date of acquisition.

Accretion of Deferred Gain on Sale Leaseback

On October 25, 2006, we, along with our wholly-owned subsidiary Nexus, entered into an agreement with Slough for the sale of our real property located in San Diego, California for a purchase price of $47.6 million. This property, with a net book value of $14.5 million, includes one building totaling approximately 82,500 square feet, the land on which the building is situated, and two adjacent vacant lots. As part of the sale transaction, we agreed to lease back the building for a period of 15 years. The sale transaction subsequently closed on November 9, 2006.

In accordance with SFAS 13, Accounting for Leases , we recognized an immediate pre-tax gain on the sale transaction of $3.1 million in the fourth quarter of 2006 and deferred a gain of $29.5 million on the sale of the building. The deferred gain is recognized as an offset to operating expense on a straight-line basis over the 15 year term of the lease at a rate of approximately $2.0 million per year.

Interest Income

Interest income was $2.1 million for 2008, compared to $8.7 million for 2007 and $3.8 million for 2006. The decrease from 2007 to 2008 is due to lower cash and investment balances as a result of the $252.7 million cash dividend paid on April 19, 2007, as well as lower interest rates. The increase from 2006 to 2007 is primarily due to higher cash and investment balances as a result of the proceeds from the sale of the Oncology Product Line in October 2006, the sale and leaseback of the corporate headquarters in November 2006 and the sale of the AVINZA Product Line in February 2007.

 

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Income Taxes

During 2008, we had losses from continuing operations and discontinued operations. For 2007 and 2006, we had losses from continuing operations and income from discontinued operations. Our overall 2008 net income tax benefit consists of an income tax benefit of $0.4 million from discontinued operations and an income tax benefit of $0.06 million from continuing operations. The net tax benefit reflects current federal and state tax refunds and a foreign tax receivable. In accordance with SFAS No. 109, Accounting for Income Taxes , the losses from continuing operations in 2007 and 2006 generated benefits of $18.7 million and $18.8 million, respectively. This income tax benefit captures the deemed use of losses from continuing operations used to offset the income and gain from our AVINZA Product Line and Oncology Product Line that were sold in 2007 and 2006, respectively.

At December 31, 2008, we have federal net operating loss carryforwards of $398.4 million, $130.0 million of state net operating loss carryforwards and $22.4 million of federal research and development credit carryforwards. Federal research and development credit carryforwards of $1.0 million expired at the beginning of 2009 with the remainder expiring through 2028, and we have $13.0 million of California and New Jersey research and development credit carryforwards that have no expiration date.

Pursuant to Internal Revenue Code Sections 382 and 383, use of net operating loss and credit carryforwards may be limited if there were changes in ownership of more than 50%. We have completed a Section 382 study for Ligand, excluding Glycomed, and have determined that Ligand had an ownership change in 2005 and 2007. As a result of these ownership changes, utilization of Ligand’s net operating losses and credits are subject to limitations under Internal Revenue Code Sections 382 and 383. The information necessary to determine if an ownership change related to Glycomed occurred prior to its acquisition by Ligand is not currently available. Accordingly, such tax net operating loss and credit carryforwards are not reflected in our deferred tax assets. If information becomes available in the future to substantiate the ability to utilize these net operating losses not limited by Sections 382, we will record the deferred tax assets at such time.

Our research and development credits pertain to federal, California and New Jersey jurisdictions. These jurisdictions require that we create minimal documentation and support. We completed a formal study and believe that we maintains sufficient documentation to support the amounts of the research and development credits.

Discontinued Operations

Oncology Product Line

On September 7, 2006, we and Eisai entered into the Oncology purchase agreement pursuant to which Eisai agreed to acquire all of our worldwide rights in and to our oncology products, or Oncology Product Line, including, among other things, all related inventory, equipment, records and intellectual property, and assume certain liabilities as set forth in the Oncology purchase agreement. The Oncology Product Line included our four marketed oncology drugs: ONTAK, Targretin capsules, Targretin gel and Panretin gel. Pursuant to the Oncology purchase agreement, at closing on October 25, 2006, we received $185.0 million in net cash proceeds, which is net of $20.0 million that was funded into an escrow account to support any potential indemnification claims made by Eisai following the closing of the sale. Of the escrowed amount, $10.0 million was released to us on April 25, 2007, and the remaining $10.0 million, plus interest of $0.8 million, was released to us on October 25, 2007. We also recorded $1.7 million in transaction fees and costs associated with the sale that are not reflected in net cash proceeds. We recorded a pre-tax gain on the sale of $135.8 million in the fourth quarter of 2006. In 2007, we recognized a $20.8 million pre-tax gain resulting from the release of funds from the escrow account partially offset by a $2.8 million pre-tax loss due to subsequent changes in certain estimates of assets and liabilities recorded as of the sale date. In 2008, we recognized a $10.6 million pre-tax loss resulting from the Salk settlement for $13.0 million partially offset by a $2.4 million pre-tax gain due to subsequent changes in certain estimates of assets and liabilities recorded as of the sale date.

 

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Additionally, $38.6 million of the proceeds received from Eisai were deposited into an escrow account to repay a loan received from King Pharmaceuticals, Inc., or King, the proceeds of which were used to pay our co-promote termination obligation to Organon in October 2006. The escrow amounts were released and the loan repaid to King in January 2007.

In connection with the Oncology purchase agreement with Eisai, we entered into a transition services agreement whereby we agreed to perform certain transition services for Eisai, in order to effect, as rapidly as practicable, the transition of purchased assets from Ligand to Eisai. In exchange for these services, Eisai paid us a monthly service fee through June 25, 2007. Fees earned under the transition services agreement during 2007 and 2006, which were recorded as an offset to operating expenses, were $2.7 million and $1.9 million, respectively.

Prior to the Oncology sale, we recorded accruals for rebates, chargebacks, and other discounts related to Oncology products when product sales were recognized as revenue under the sell-through method. Upon the Oncology sale, we accrued for rebates, chargebacks, and other discounts related to Oncology products in the distribution channel which had not sold-through at the time of the Oncology sale and for which we retained the liability subsequent to the Oncology sale. These products expired at various dates through July 31, 2008. Our accruals for Oncology rebates, chargebacks, and other discounts total $0.4 million and $1.2 million as of December 31, 2008 and 2007, respectively, and they are included in accrued liabilities in the accompanying consolidated balance sheet.

Additionally, and pursuant to the terms of the Oncology purchase agreement, we retained the liability for returns of product from wholesalers that had been sold by us prior to the close of the transaction. Accordingly, as part of the accounting for the gain on the sale of the Oncology Product Line, we recorded a reserve for Oncology product returns. Under the sell-through revenue recognition method, we previously did not record a reserve for returns from wholesalers. Oncology products sold by us may be returned through a specified period subsequent to the product expiration date, but no later than July 31, 2009. Our reserve for Oncology returns was $0.9 million and $4.4 million as of December 31, 2008 and 2007, respectively, and is included in accrued liabilities in the accompanying consolidated balance sheet.

AVINZA Product Line

On September 6, 2006, we and King entered into the AVINZA purchase agreement pursuant to which King agreed to acquire all of our rights in and to AVINZA in the United States, its territories and Canada, including, among other things, all AVINZA inventory, records and related intellectual property, and assume certain liabilities as set forth in the AVINZA purchase agreement, which we collectively refer to as the Transaction. In addition, King, subject to the terms and conditions of the AVINZA purchase agreement, agreed to offer employment following the closing of the Transaction, or Closing, to certain of our existing AVINZA sales representatives or otherwise reimburse us for agreed upon severance arrangements offered to any such non-hired representatives.

Pursuant to the AVINZA purchase agreement, at Closing on February 26, 2007, or Closing Date, we received $280.4 million in net cash proceeds, which is net of $15.0 million that was funded into an escrow account to support any potential indemnification claims made by King following the Closing. Of the escrowed amount, $7.5 million was released to us on August 26, 2007, and the remaining $7.5 million, plus interest of $0.5 million, was released to us on February 26, 2008.

The net cash received also includes reimbursement of $47.8 million for co-promote termination payments which had previously been paid to Organon, $0.9 million of interest we paid King on a loan that was repaid in January 2007 and $0.5 million of severance expense for AVINZA sales representatives not offered positions with

 

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King. A summary of the final net cash proceeds, exclusive of $6.6 million in transaction costs and adjusted to reflect the final results of the retail inventory study, is as follows (in thousands):

 

Purchase price

   $ 265,000  

Reimbursement of Organon payments

     47,750  

Repayment of interest on King loan

     883  

Reimbursement of sales representative severance costs

     453  
        
     314,086  

Less retail pharmacy inventory adjustment

     (11,225 )

Less cost of goods manufacturing adjustment

     (6,000 )
        

Net cash proceeds

   $ 296,861  
        

King also assumed our co-promote termination obligation to make payments to Organon based on net sales of AVINZA ($58.5 million and $59.5 million as of December 31, 2008 and 2007, respectively). As Organon has not consented to the legal assignment of the co-promote termination obligation from us to King, we remain liable to Organon in the event of King’s default of this obligation. We also incurred $6.6 million in transaction fees and other costs associated with the sale that are not reflected in the net cash proceeds, of which $3.6 million was recognized in 2006. We recorded a pre-tax gain on the sale of $310.1 million in the first quarter of 2007. We recorded a $0.3 million pre-tax increase to the gain on the sale in the second quarter of 2007 due to subsequent changes in certain estimates of assets and liabilities recorded as of the sale date partially offset by an adjustment to investment banking fees. In the third quarter of 2007, we recognized a $7.5 million pre-tax gain resulting from the release of funds from the escrow account partially offset by a $0.6 million pre-tax loss due to subsequent changes in certain estimates of assets and liabilities recorded as of the sale date. We recorded a $2.1 million pre-tax decrease to the gain on the sale in the fourth quarter of 2007 due to subsequent changes in certain estimates of assets and liabilities recorded as of the sale date. In 2008, we recognized an $8.1 million pre-tax gain resulting from the release of funds from the escrow account. In addition, during 2008 we recognized a $1.5 million pre-tax gain due to subsequent changes in certain estimates of assets and liabilities recorded as of the sale date.

Also on September 6, 2006, we entered into a contract sales force agreement, or sales call agreement, with King, pursuant to which King agreed to conduct a sales detailing program to promote the sale of AVINZA for an agreed upon fee, subject to the terms and conditions of the sales call agreement. Pursuant to the Sales Call Agreement, King agreed to perform certain minimum monthly product details (i.e. sales calls), which commenced effective October 1, 2006 and continued until the Closing Date. Co-promotion expense recognized under the sales call agreement for 2007 and 2006 was $2.8 million and $3.8 million, respectively. No amount was due to King under the sales call agreement as of December 31, 2007. The sales call agreement terminated effective on the Closing Date.

Prior to the AVINZA sale, we recorded accruals for rebates, chargebacks, and other discounts related to AVINZA products when product sales were recognized as revenue under the sell-through method. Upon the AVINZA sale, we accrued for rebates, chargebacks, and other discounts related to AVINZA products in the distribution channel which had not sold-through at the time of the AVINZA sale and for which we retained the liability subsequent to the sale. These products expire at various dates through June 30, 2009. Our accruals for AVINZA rebates, chargebacks, and other discounts total $0.1 million and $1.0 million as of December 31, 2008 and 2007, respectively, and are included in accrued liabilities in the accompanying consolidated balance sheets.

Additionally, and pursuant to the terms of the AVINZA purchase agreement, we retained the liability for returns of product from the distribution channel that had been sold by us prior to the close of the transaction. Accordingly, as part of the accounting for the gain on the sale of AVINZA, we recorded a reserve for AVINZA product returns. Under the sell-through revenue recognition method, we previously did not record a reserve for returns. AVINZA products sold by us may be returned through a specified period subsequent to the product

 

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expiration date, but no later than December 31, 2009. Our reserve for AVINZA returns is $8.2 million and $10.7 million as of December 31, 2008 and 2007, respectively, and is included in accrued liabilities in the accompanying consolidated balance sheet.

Summary of Results from Discontinued Operations

There were no activities related to discontinued operations in 2008. Income from discontinued operations before income taxes was $6.0 million in 2007 compared to a loss from discontinued operations before income taxes of $91.4 million in 2006.

The following table summarizes the 2007 results from discontinued operations included in the 2007 consolidated statement of operations (in thousands):

 

     AVINZA
Product
Line

Product sales

   $ 18,256
      

Operating costs and expenses:

  

Cost of products sold

     3,608

Research and development

     120

Selling, general and administrative

     3,709

Co-promotion

     2,814

Co-promote termination charges

     2,012
      

Total operating costs and expenses

     12,263
      

Income from operations

     5,993

Interest expense

     —  
      

Income before income taxes

   $ 5,993
      

The following table summarizes the 2006 results from discontinued operations included in the 2006 consolidated statement of operations (in thousands):

 

     Oncology
Product
Line
    AVINZA
Product
Line
    Total  

Product sales

   $ 47,512     $ 136,983     $ 184,495  

Collaborative research and development and other revenues

     208       —         208  
                        

Total revenues

     47,720       136,983       184,703  
                        

Operating costs and expenses:

      

Cost of products sold

     13,410       22,642       36,052  

Research and development

     12,895       380       13,275  

Selling, general and administrative

     13,891       36,118       50,009  

Co-promotion

     —         37,455       37,455  

Co-promote termination charges

     —         131,078       131,078  
                        

Total operating costs and expenses

     40,196       227,673       267,869  
                        

Income (loss) from operations

     7,524       (90,690 )     (83,166 )

Interest expense

     (51 )     (8,187 ) (1)     (8,238 )
                        

Income (loss) before income taxes

   $ 7,473     $ (98,877 )   $ (91,404 )
                        

 

(1) As part of the terms of the AVINZA purchase agreement, we were required to redeem its outstanding convertible subordinated notes. All of the notes converted into shares of common stock in 2006 prior to redemption. In accordance with EITF 87-24, Allocation of Interest to Discontinued Operations , the interest on the notes was allocated to discontinued operations because the debt was required to be repaid in connection with the disposal transaction.

 

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Product sales were $18.3 million in 2007 compared to $184.5 million in 2006. Total operating costs were $12.3 million in 2007 compared to $267.9 million in 2006. The decrease in product sales and total operating costs and expenses in 2007 compared to 2006 was primarily due to the sales of the Oncology and AVINZA Product Lines effective October 25, 2006 and February 26, 2007, respectively.

Co-promotion expense of $2.8 million in 2007 represents fees paid to King for contract sales expenses incurred under the sales call agreement prior to the closing of the Transaction on February 26, 2007. This compares to $37.5 million of co-promotion expense recognized under our co-promotion arrangement with Organon in 2006 that concluded September 30, 2006.

In 2006, we recognized $131.1 million of co-promote termination costs in connection with the termination of our AVINZA co-promote arrangement with Organon effective January 1, 2006. In 2007, we recognized $2.0 million of co-promote termination expense which represents the accretion of the termination liability to fair value as of February 26, 2007, the closing of the AVINZA Product Line sale Transaction.

Interest expense in 2006 of $8.2 million primarily represented interest on our then outstanding convertible subordinated notes. As part of the terms of the AVINZA purchase agreement, we were required to redeem the outstanding notes. All of the notes converted into shares of common stock in 2006 prior to redemption. In accordance with EITF 87-24, Allocation of Interest to Discontinued Operations , the interest on the notes was allocated to discontinued operations because the debt was required to be repaid in connection with the disposal transaction.

Liquidity and Capital Resources

We have financed our operations through private and public offerings of our equity securities, collaborative research and development and other revenues, issuance of convertible notes, product sales and the subsequent sales of our commercial assets, capital and operating lease transactions, accounts receivable factoring and equipment financing arrangements and investment income. In March 2007, we announced that our board of directors authorized a stock repurchase program under Rule 10b-18 of the Securities Exchange Act of 1934, as amended, of up to $100 million of shares of our common stock in the open market and negotiated purchases over a period of 12 months. In 2008 and 2007, we repurchased 0.3 million and 6.2 million shares, respectively, of our common stock in open market transactions at varying prices for an aggregate purchase price of $1.6 million and $39.6 million.

Working capital was $23.3 million at December 31, 2008 compared with $59.0 million at December 31, 2007. Cash, cash equivalents and short-term investments total $80.7 million as of December 31, 2008 compared with $94.4 million as of December 31, 2007. We primarily invest our cash in United States government and investment grade corporate debt securities.

On July 19, 2007, we purchased $5.0 million of commercial paper issued by Golden Key Ltd. While the investment was highly-rated and within our investment policy at the time of purchase, during the third quarter of 2007, large credit rating agencies downgraded the quality of this security. In addition, as a result of not meeting certain liquidity covenants, the assets were assigned to a trustee who established a committee of the largest senior credit holders to determine the next steps. Subsequently, Golden Key defaulted on its obligation to settle the security on the stated maturity date of October 10, 2007. Based on available information, we estimate that we will be able to recover approximately $1.7 million on this security. Accordingly, we adjusted the carrying value by recording impairment losses of $2.0 million and $1.3 million during the years ended December 31, 2008 and 2007, respectively. Further, liquidity in the capital markets has continued to be volatile. Accordingly, we may be exposed to additional impairment for this investment until it is fully recovered.

 

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Based on our current business outlook, we believe our currently available cash, cash equivalents, and short-term investments as well as our current and future royalty revenues will be sufficient to satisfy our anticipated operating and capital requirements through at least the next twelve months. Our future operating and capital requirements will depend on many factors, including, but not limited to: the pace of scientific progress in our research and development programs; the magnitude of these programs; the scope and results of preclinical testing and clinical trials; the time and costs involved in obtaining regulatory approvals; the costs involved in preparing, filing, prosecuting, maintaining and enforcing patent claims; competing technological and market developments; the amount of royalties on sales of AVINZA and PROMACTA; and the efforts of our collaborative partners. We will also consider additional equipment financing arrangements similar to arrangements currently in place.

Operating Activities

Operating activities used cash of $20.6 million, $97.7 million and $138.5 million in 2008, 2007 and 2006, respectively. The use of cash in 2008 reflects a net loss of $98.1 million, adjusted by $0.7 million of loss from discontinued operations and $82.7 million of non-cash items to reconcile the net loss to net cash used in operations. These reconciling items primarily reflect the write-off of acquired in-process research and development of $72.0 million, non-cash exit and restructuring costs of $5.3 million, the recognition of $3.6 million of stock-based compensation expense, depreciation of assets of $1.1 million, realized loss on investment of $2.0 million, and the write-off of assets of $0.7 million, partially offset by the accretion of deferred gain on the sale leaseback of the building of $2.0 million. The use of cash in 2008 is further impacted by changes in operating assets and liabilities due primarily to decreases in accounts payable and accrued liabilities of $7.3 million partially offset by decreases in other current assets of $4.9 million and an increase in other liabilities of $1.3 million. Net cash used in operating activities of discontinued operations was $4.6 million in 2008.

The use of cash in 2007 reflects net income of $281.7 million, adjusted by $316.4 million of gain from discontinued operations and $11.0 million of non-cash items to reconcile net income to net cash used in operations. These reconciling items primarily reflect deferred gain on the sale leaseback of the building of $2.0 million, the recognition of $7.6 million of stock-based compensation expense, depreciation and amortization of assets of $2.6 million, a realized loss on investment of $1.3 million, and the write-off of assets of $1.0 million. The use of cash in 2007 is further impacted by changes in operating assets and liabilities due primarily to decreases in accounts payable and accrued liabilities of $54.5 million and to deferred revenue of $8.7 million and an increase in the restricted indemnity account of $10.1 million, partially offset by decreases in accounts receivable, net of $11.5 million, other current assets of $1.4 million, and inventories, net of $0.9 million. The increase in the restricted indemnity account is primarily due to the funding of $10.0 million to support our existing indemnification obligations to continuing and departing directors in connection with the ongoing SEC investigation and related matters. Net cash used in operating activities from discontinued operations was $15.6 million in 2007.

The use of cash in 2006 reflects a net loss of $31.7 million, adjusted by $24.8 million of gain from discontinued operations and $18.3 million of non-cash items to reconcile the net loss to net cash used in operations. These reconciling items include depreciation and amortization of assets of $16.2 million and the recognition of $5.3 million of stock-based compensation expense partially offset by gain on sale leaseback of $3.1 million. The use of cash in 2006 is further impacted by changes in operating assets and liabilities due primarily to decreases in accounts payable and accrued liabilities of $26.6 million partially offset

 

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by decreases in accounts receivable, net of $9.4 million; inventories of $1.6 million; and other current assets of $6.6 million. Net cash used in operating activities of discontinued operations was $91.3 million in 2006.

Investing Activities

Investing activities used cash of $24.4 million in 2008 and provided cash of $343.8 million and $196.9 million in 2007 and 2006, respectively. Cash used in investing activities in 2008 primarily reflects the net purchases of short-term investments of $36.4 million partially offset by $4.1 million of net cash acquired from our merger with Pharmacopeia. Net cash provided by investing activities of discontinued operations was $8.1 million in 2008.

Cash provided by investing activities in 2007 primarily reflects the net purchases of short-term investments of $5.4 million partially offset by the decrease in restricted cash and investments of $1.5 million. Net cash provided by investing activities of discontinued operations was $347.9 million in 2007.

Cash provided by investing activities in 2006 includes proceeds from the sale leaseback of our corporate headquarters of $46.9 million and net proceeds from the sale of short-term investments of $7.2 million. These amounts were partially offset by an increase in restricted cash and investments of $1.1 million and purchases of property and equipment of $1.8 million. Net cash provided by investing activities of discontinued operations was $145.6 million in 2006.

Financing Activities

Financing activities used cash of $3.0 million and $327.7 million in 2008 and 2007, respectively, and provided cash of $33.3 million in 2006. Cash used in financing activities in 2008 primarily reflects repurchase of our common stock of $1.6 million and payments under equipment financing obligations of $1.5 million.

Cash used in financing activities in 2007 primarily reflects the $252.7 million cash dividend payment, $39.6 million in repurchases of our common stock, and payments under equipment financing obligations of $2.2 million. These amounts are partially offset by proceeds from the issuance of common stock, related primarily to the exercise of employee stock options, of $4.4 million. Net cash used in financing activities of discontinued operations was $37.8 million in 2007.

 

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Cash provided by financing activities in 2006 includes the repayment of the mortgage note payable due on our corporate headquarters of $11.8 million in connection with the sale of that building in November 2006, and net payments under equipment financing arrangements of $1.5 million partially offset by proceeds from the exercise of employee stock options and stock purchases of $9.1 million. Net cash provided by financing activities of discontinued operations was $37.8 million in 2006.

Other

As part of our alliances with GSK, Wyeth, Cephalon and Schering-Plough and our discovery collaboration agreement with BMS, we have received up-front cash payments and licenses to certain product candidates. In connection with these agreements, we are obligated to perform significant research and development activities over multiple years and as such, expect to incur significant costs performing such activities. The following table provides the period over which these research and development activities are to be provided, as well as the deferred revenue currently recorded for each agreement as of December 31, 2008:

 

Collaborative Agreement

   Expiration of
Initial Research Term
   Deferred Revenue

2007 Schering-Plough Agreement

   February 2012    $ 3,492

BMS Discovery Collaboration Agreement

   December 2011      13,003

GSK Agreement

   March 2011      6,250

Wyeth Agreement

   December 2009      1,510

Cephalon Agreement

   May 2009      319

On March 22, 2007, we announced a return of cash on our common stock in the form of a $2.50 per share special cash dividend. The aggregate amount of $252.7 million was paid on April 19, 2007 to shareholders of record as of April 5, 2007. In addition to the cash dividend, the Board of Directors authorized up to $100.0 million in share repurchases over the subsequent 12 months. In 2007, we repurchased 6.2 million shares of our common stock totaling $39.6 million. Subsequent to December 31, 2007 and through February 28, 2008, we repurchased an additional 0.3 million shares of our common stock totaling $1.6 million. We currently have no plans of issuing any dividends or repurchasing additional shares of our common stock in the near future.

Certain of our property and equipment is pledged as collateral under various equipment financing arrangements. As of December 31, 2008, $4.0 million was outstanding under such arrangements with $1.8 million classified as current. During January 2009, we paid off the remaining $3.4 million of financing obligations acquired through our acquisition of Pharmacopeia.

On July 19, 2007, we purchased $5.0 million of commercial paper issued by Golden Key Ltd. While the investment was highly-rated and within our investment policy at the time of purchase, during the third quarter of 2007, large credit rating agencies downgraded the quality of this security. In addition, as a result of not meeting certain liquidity covenants, the assets were assigned to a trustee who established a committee of the largest senior credit holders to determine the next steps. Subsequently, Golden Key defaulted on its obligation to settle the security on the stated maturity date of October 10, 2007. Based on available information, we estimate that we will be able to recover approximately $1.7 million on this security. Accordingly, we adjusted the carrying value by recording an impairment loss of $2.0 million and $1.3 million in December 2008 and 2007, respectively. Further, liquidity in the capital markets has continued to be volatile. Accordingly, we may be exposed to additional impairment for this investment until it is fully recovered.

The noteholders of our 6% convertible subordinated notes, in the aggregate principal amount of $155.3 million, converted all of the notes into approximately 25.1 million shares of our common stock in 2006. Accrued interest and unamortized debt issue costs related to the converted notes of $0.5 million and $1.4 million, respectively, were recorded as additional paid-in capital.

 

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In connection with the acquisition of Pharmacopeia on December 23, 2008, Pharmacopeia security holders received a contingent value right that entitles them to an aggregate cash payment of $15.0 million under certain circumstances.

Leases and Off-Balance Sheet Arrangements

We lease our office and research facilities under operating lease arrangements with varying terms through November 2021. The agreements provide for increases in annual rents based on changes in the Consumer Price Index or fixed percentage increases ranging from 3% to 7%. Commencing January 2008, we also sublease a portion of our facilities through July 2015. The sublease agreement provides for a 3% increase in annual rents.

Contractual Obligations

As of December 31, 2008, future minimum payments due under our contractual obligations are as follows (in thousands):

 

     Payments Due by Period
     Total    Less than
1 year
   1-3 years    3-5 years    More than
5 years

Equipment financing obligations (1)

   $ 4,506    $ 2,141    $ 2,349    $ 16    $ —  

Operating lease obligations (2)

     83,154      7,815      16,094      16,743      42,502

Severance obligation

     846      846      —        —        —  

Consulting / License Agreements

     1,369      1,019      200      150      —  

Co-promote termination liability (3)

     —        —        —        —        —  
                                  

Total contractual obligations

   $ 89,875    $ 11,821    $ 18,643    $ 16,909    $ 42,502
                                  

 

(1)    Includes interest payments as follows:

   $ 500    $ 313    $ 187    $ —      $ —  
(2) We lease an office and research facility under an operating lease arrangement through July 2015. Commencing January 2008, we sublet this facility through July 2015. The sublease agreement provides for a 3% increase in annual rents. As of December 31, 2008, we expect to receive aggregate future minimum lease payments totaling $5.7 million (nondiscounted) over the duration of the sublease agreement as follows and not included in the table above: less than one year, $0.8 million; one to three years, $1.7 million; three to five years, $1.8 million; and more than five years, $1.4 million.
(3) Our co-promote termination obligation to Organon was assumed by King pursuant to the AVINZA purchase agreement. However, as Organon did not consent to the legal assignment of the obligation to King, Ligand remains liable to Organon in the event of King’s default of the obligation. As of December 31, 2008, the total estimated amount of the obligation is $58.5 million on an undiscounted basis. We do not expect to make any cash payments related to this obligation.

As of December 31, 2008, we have net open purchase orders (defined as total open purchase orders at year end less any accruals or invoices charged to or amounts paid against such purchase orders) totaling approximately $7.4 million. We plan to spend approximately $0.8 million on capital expenditures in 2009.

 

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Critical Accounting Policies

Certain of our policies require the application of management judgment in making estimates and assumptions that affect the amounts reported in the consolidated financial statements and disclosures made in the accompanying notes. Those estimates and assumptions are based on historical experience and various other factors deemed to be applicable and reasonable under the circumstances. The use of judgment in determining such estimates and assumptions is by nature, subject to a degree of uncertainty. Accordingly, actual results could differ materially from the estimates made. Our critical accounting policies are as follows:

Revenue Recognition

Royalties on sales of AVINZA and PROMACTA are recognized in the quarter reported by the respective partner.

Revenue from research funding under our collaboration agreements is earned and recognized on a percentage of completion basis as research hours are incurred in accordance with the provisions of each agreement.

Revenue earned related to up-front product and technology license fees is recognized in accordance with Staff Accounting Bulletin 104 issued by the SEC and Emerging Issue Task Force (EITF) Issue 00-21, “Revenue Arrangements with Multiple Deliverables” issued by the Financial Accounting Standards Board, or the FASB. Accordingly, amounts received under multiple-element arrangements requiring ongoing services or performance by us are recognized over the period of such services or performance.

Revenue from milestones is recognized when earned, as evidenced by written acknowledgement from the collaborator, provided that (i) the milestone event is substantive and its achievability was not reasonably assured at the inception of the agreement, (ii) we have no further performance obligations relating to that event, and (iii) collectibility is reasonably assured. If these criteria are not met, the milestone payment is recognized over the remaining minimum period of our performance obligations under the arrangement.

Co-Promote Termination Accounting

As part of the termination and return of co-promotion rights agreement that we entered into with Organon in January 2006, we agreed to make quarterly payments to Organon, effective for the fourth quarter of 2006, equal to 6.5% of AVINZA net sales through December 31, 2012 and thereafter 6% through patent expiration, currently anticipated to be November 2017. The estimated fair value of the amounts to be paid to Organon after the termination ($95.2 million as of January 2006), based on the future estimated net sales of the product, was recognized as a liability and expensed as a cost of the termination as of the effective date of the agreement, January 2006.

In connection with the AVINZA sale transaction, King assumed our obligation to make payments to Organon based on net sales of AVINZA (the fair value of which approximated $58.5 million as of December 31, 2008). As Organon has not consented to the legal assignment of the co-promote termination obligation from us to King, we remain liable to Organon in the event of King’s default of this obligation. Therefore, we recorded an asset on February 26, 2007 to recognize King’s assumption of the obligation, while continuing to carry the co-promote termination liability in our consolidated financial statements to recognize our legal obligation as primary obligor to Organon as required under SFAS No. 140, Accounting for Transfers and Servicing of Financial Assets and Extinguishments of Liabilities . This asset represents a non-interest bearing receivable for future payments to be made by King and is recorded at its fair value. As of December 31, 2008 and thereafter, the receivable and liability will remain equal and adjusted each quarter for changes in the fair value of the obligation. On a quarterly basis, management reviews the carrying value and assesses the co-promote termination receivable for impairment (e.g. in the event King defaults on the assumed obligation to pay Organon). Annually

 

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management also reviews the carrying value of the co-promote termination liability. Due to assumptions and judgments inherent in determining the estimates of future net AVINZA sales through November 2017, the actual amount of net AVINZA sales used to determine the amount of the asset and liability for a particular period may be materially different from current estimates. Any resulting changes to the co-promote termination liability will have a corresponding impact on the co-promote termination payments receivable. As of December 31, 2008 and 2007, the fair value of the co-promote termination liability (and the corresponding receivable) was determined using a discount rate of 15%.

Impairment of Long-Lived Assets

We review long-lived assets for impairment annually or whenever events or circumstances indicate that the carrying amount of the assets may not be recoverable. We measure the recoverability of assets to be held and used by comparing the carrying amount of an asset to future undiscounted net cash flows expected to be generated by the asset. If such assets are considered to be impaired, the impairment to be recognized is measured as the amount by which the carrying amount of the assets exceeds the fair value of the assets. Fair value of our long-lived assets is determined using the expected cash flows discounted at a rate commensurate with the risk involved. As of December 31, 2008, we believe that the future undiscounted cash flows to be received from our long-lived assets will exceed the assets’ carrying value.

Income Taxes

Income taxes are accounted for under the liability method. This approach requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of differences between the tax basis of assets or liabilities and their carrying amounts in the consolidated financial statements. A valuation allowance is provided for deferred tax assets if it is more likely than not that these items will either expire before we are able to realize their benefit or if future deductibility is uncertain. As of December 31, 2008 and 2007, we have provided a full valuation allowance against the deferred tax asset as recoverability was uncertain. Developing the provision for income taxes requires significant judgment and expertise in federal and state income tax laws, regulations and strategies, including the determination of deferred tax assets and liabilities and, if necessary, any valuation allowances that may be required for deferred tax assets. Our judgments and tax strategies are subject to audit by various taxing authorities. While we believe we have provided adequately for our income tax liabilities in our consolidated financial statements, adverse determinations by these taxing authorities could have a material adverse effect on our consolidated financial condition and results of operations.

Stock-Based Compensation

We have employee compensation plans under which various types of stock-based instruments are granted. We account for our share-based payments in accordance with SFAS No. 123(R), “ Share-Based Payment ”. This statement requires all share-based payments to employees, including grants of employee stock options, to be recognized in the Consolidated Statements of Income as compensation expense (based on their estimated fair values) generally over the vesting period of the awards.

Stock-based compensation cost for awards to employees and non-employee directors is recognized on a straight-line basis over the vesting period until the last tranche vests. Compensation cost for consultant awards is recognized over each separate tranche’s vesting period. We recognized compensation expense of $3.6 million, $7.6 million and $5.3 million for 2008, 2007 and 2006, respectively, associated with option awards, restricted stock and an equitable adjustment of employee stock options. Of the total compensation expense associated with option awards, $0.3 million related to options granted to non-employee consultants for 2006. Of the total compensation expense associated with the option awards for 2007, $1.8 million related to the $2.50 equitable adjustment of the exercise price for all options outstanding as of April 3, 2007 that was measured for financial reporting purposes effective March 28, 2007, the date our Compensation Committee of our Board of Directors approved the adjustment.

 

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The fair-value for options that were awarded to employees and directors was estimated at the date of grant using the Black-Scholes option valuation model with the following weighted average assumptions:

 

     Years Ended December 31,  
     2008     2007     2006  

Risk-free interest rate

   3.0 %   4.9 %   4.8 %

Dividend yield

   —       —       —    

Expected volatility

   65 %   66 %   70 %

Expected term

   6 years     6 years     6 years  

The expected term of the employee and non-employee director options is the estimated weighted-average period until exercise or cancellation of vested options (forfeited unvested options are not considered). SAB 107 guidance permits companies to use a “safe harbor” expected term assumption for grants up to December 31, 2007 based on the mid-point of the period between vesting date and contractual term, averaged on a tranche-by-tranche basis. We used the safe harbor in selecting the expected term assumption in 2008 and 2007. The expected term for consultant awards is the remaining period to contractual expiration.

Volatility is a measure of the expected amount of variability in the stock price over the expected life of an option expressed as a standard deviation. SFAS 123(R) requires an estimate of future volatility. In selecting this assumption, we used the historical volatility of our stock price over a period equal to the expected term. Changes in the assumptions used to estimate the fair value of stock-based compensation would impact the amount of compensation expenses recognized during the period.

New Accounting Pronouncements

In September 2006, the FASB issued SFAS No. 157, Fair Value Measurements, or SFAS 157. SFAS 157 defines fair value, establishes a framework for measuring fair value under GAAP, and expands disclosures about fair value measurements. SFAS 157 does not require any new fair value measurements but rather eliminates inconsistencies in guidance found in various prior accounting pronouncements and is effective for financial statements issued for fiscal years beginning after November 15, 2007. In February 2008, the FASB issued FASB FSP 157-2 which delays the effective date of SFAS 157 for all nonfinancial assets and nonfinancial liabilities, except those that are recognized or disclosed at fair value in the financial statements on a recurring basis (at least annually), until fiscal years beginning after November 15, 2008, and interim periods within those fiscal years. These nonfinancial items include assets and liabilities such as reporting units measured at fair value in a goodwill impairment test and nonfinancial assets acquired and liabilities assumed in a business combination. Effective January 1, 2008, we adopted SFAS 157 for financial assets and liabilities recognized at fair value on a recurring basis. The adoption of SFAS 157 did not have a material impact on our consolidated results of operations or financial position.

In December 2007, the FASB issued SFAS No. 141 (revised 2007), Business Combinations , or SFAS 141R. SFAS 141R requires an acquirer to (i) recognize the assets acquired, liabilities assumed, contractual contingencies, and contingent consideration at fair value at the acquisition date, (ii) recognize acquisition-related costs separately from the acquisition, (iii) to recognize “negative goodwill” in earnings as a gain attributable to the acquisition, and (iv) to recognize changes in the amount of its deferred tax benefits that are recognizable because of the business combination either in earnings in the period of the combination or directly in contributed capital, depending on the circumstances. SFAS 141R is effective for business combinations for which the acquisition date is on or after the beginning of the first annual reporting period beginning on or after December 15, 2008 and, as such, will be applied prospectively for business combinations that occur on or after January 1, 2009.

In December 2007, the FASB issued Statement No. 160, Noncontrolling Interests in Consolidated Financial Statements—an amendment of ARB No. 51 , or SFAS 160. SFAS 160 requires entities to present ownership

 

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interests in subsidiaries held by parties other than the parent entity within the equity section of the consolidated balance sheet, to present the amount of consolidated net income attributable to the parent and to the noncontrolling interest in the consolidated statement of operations, to recognize any changes in ownership interests as equity transactions, and to measure at fair value any retained noncontrolling equity investment upon deconsolidation of a subsidiary. We will adopt SFAS 160 in the first interim period of fiscal 2009, and management is evaluating the impact, if any, that the adoption of this statement will have on its consolidated results of operations and financial position.

In March 2008, the FASB issued Statement No. 161, Disclosures about Derivative Instruments and Hedging Activities —an amendment of FASB Statement No. 133 , or SFAS 161. SFAS 161 requires entities to disclose the objectives for using derivative instruments in terms of underlying risk and accounting designation, to disclose the fair values of derivative instruments and their gains and losses in a tabular format, and to disclose information about credit-risk-related contingent features. We will adopt SFAS 161 in the first interim period of fiscal 2009, and management is evaluating the impact, if any, that the adoption of this statement will have on its consolidated results of operations and financial position.

 

Item 7A. Quantitative and Qualitative Disclosures About Market Risk

At December 31, 2008, our investment portfolio included fixed-income securities of $53.3 million. These securities are subject to interest rate risk and will decline in value if interest rates increase. However, due to the short duration of our investment portfolio, an immediate 10% change in interest rates would have no material impact on our financial condition, results of operations or cash flows. At December 31, 2008, we also have certain equipment financing arrangements with variable rates of interest. Due to the relative insignificance of such arrangements, however, an immediate 10% change in interest rates would have no material impact on our financial condition, results of operations, or cash flows. Declines in interest rates over time will, however, reduce our interest income, while increases in interest rates over time will increase our interest expense.

We do not have a significant level of transactions denominated in currencies other than U.S. dollars and as a result we have very limited foreign currency exchange rate risk. The effect of an immediate 10% change in foreign exchange rates would have no material impact on our financial condition, results of operations or cash flows.

 

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Item 8. Consolidated Financial Statements and Supplementary Data

INDEX TO CONSOLIDATED FINANCIAL STATEMENTS

 

     Page

Report of Independent Registered Public Accounting Firm—Grant Thornton LLP

   58

Report of Independent Registered Public Accounting Firm—BDO Seidman, LLP

   59

Consolidated Balance Sheets

   60

Consolidated Statements of Operations

   61

Consolidated Statements of Stockholders’ Equity (Deficit) and Comprehensive Income (Loss)

   62

Consolidated Statements of Cash Flows

   63

Notes to Consolidated Financial Statements

   64

 

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REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

The Board of Directors and Stockholders

Ligand Pharmaceuticals Incorporated

We have audited the accompanying consolidated balance sheet of Ligand Pharmaceuticals Incorporated (the Company) as of December 31, 2008, and the related consolidated statements of operations, stockholders’ equity (deficit) and comprehensive income (loss) and cash flows for the year then ended. Our audit of the basic consolidated financial statements included the financial statement schedule listed in the index appearing under Item 15(4)(d). These consolidated financial statements and schedule are the responsibility of the Company’s management. Our responsibility is to express an opinion on these financial statements and schedule based on our audit.

We conducted our audit in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement. An audit includes examining, on a test basis, evidence supporting the amounts and disclosures in the financial statements. An audit also includes assessing the accounting principles used and significant estimates made by management, as well as evaluating the overall financial statement presentation. We believe that our audit provides a reasonable basis for our opinion.

In our opinion, the consolidated financial statements referred to above present fairly, in all material respects, the financial position of Ligand Pharmaceuticals Incorporated as of December 31, 2008, and the results of its operations and its cash flows for the year then ended in conformity with accounting principles generally accepted in the United States of America. Also, in our opinion, the related financial statement schedule, when considered in relation to the basic consolidated financial statements taken as a whole, presents fairly, in all material respects, the information set forth therein.

We have also audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States), Ligand Pharmaceuticals Incorporated’s internal control over financial reporting as of December 31, 2008, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO) and our report dated March 13, 2009 expressed an unqualified opinion.

/s/ Grant Thornton LLP

San Diego, California

March 13, 2009

 

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REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

The Board of Directors and Stockholders

Ligand Pharmaceuticals Incorporated

San Diego, California

We have audited the accompanying consolidated balance sheet of Ligand Pharmaceuticals Incorporated and subsidiaries (the “Company”) as of December 31, 2007, and the related consolidated statements of operations, stockholders’ equity (deficit) and comprehensive income (loss), and cash flows for each of the two years in the period ended December 31, 2007. We have also audited Schedule II – Valuation and Qualifying Accounts for the two years ended December 31, 2007. These consolidated financial statements and schedule are the responsibility of the Company’s management. Our responsibility is to express an opinion on these consolidated financial statements and schedule based on our audits.

We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the consolidated financial statements and schedule are free of material misstatement. An audit includes examining, on a test basis, evidence supporting the amounts and disclosures in the consolidated financial statements, assessing the accounting principles used and significant estimates made by management, as well as evaluating the overall consolidated financial statement and schedule presentation. We believe that our audits provide a reasonable basis for our opinion.

In our opinion, the consolidated financial statements referred to above present fairly, in all material respects, the financial position of Ligand Pharmaceuticals Incorporated and subsidiaries as of December 31, 2007, and the consolidated results of its operations and its cash flows for each of the two years in the period ended December 31, 2007, in conformity with accounting principles generally accepted in the United States of America. Also, in our opinion, Schedule II – Valuation and Qualifying Accounts presents fairly, in all material respects, the information set forth therein for the two years ended December 31, 2007.

/s/ BDO Seidman, LLP

San Diego, California

February 28, 2008

 

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LIGAND PHARMACEUTICALS INCORPORATED

CONSOLIDATED BALANCE SHEETS

(in thousands, except share data)

 

    December 31,  
    2008     2007  
ASSETS    

Current assets:

   

Cash and cash equivalents

  $ 28,753     $ 76,812  

Short-term investments

    51,918       17,596  

Other current assets

    2,300       5,068  

Current portion of co-promote termination payments receivable

    10,958       10,467  
               

Total current assets

    93,929       109,943  

Restricted investments

    1,341       1,411  

Property and equipment, net

    12,903       2,865  

Goodwill and other identifiable intangible assets

    5,375       —    

Long-term portion of co-promote termination payments receivable

    47,524       48,989  

Restricted indemnity account

    10,232       10,070  

Other assets

    144       —    
               

Total assets

  $ 171,448     $ 173,278  
               
LIABILITIES AND STOCKHOLDERS’ EQUITY (DEFICIT)    

Current liabilities:

   

Accounts payable

  $ 14,627     $ 12,682  

Accrued liabilities

    12,665       7,052  

Allowances for loss on returns, rebates and chargebacks related to discontinued operations

    9,590       17,275  

Current portion of accrued litigation settlement costs

    8,680       —    

Current portion of deferred gain

    1,964       1,964  

Current portion of co-promote termination liability

    10,958       10,467  

Current portion of equipment financing obligations

    1,829       1,528  

Current portion of deferred revenue

    10,301       —    
               

Total current liabilities

    70,614       50,968  

Long-term portion of co-promote termination liability

    47,524       48,989  

Long-term portion of equipment financing obligations

    2,178       627  

Long-term portion of deferred revenue, net

    16,819       2,546  

Long-term portion of deferred gain

    23,292       25,256  

Other long-term liabilities

    9,041       3,432  
               

Total liabilities

    169,468       131,818  
               

Commitments and contingencies

   

Common stock subject to conditional redemption; 997,568 shares issued and outstanding at December 31, 2008 and 2007, respectively

    12,345       12,345  
               

Stockholders’ equity (deficit):

   

Convertible preferred stock, $0.001 par value; 5,000,000 shares authorized; none issued

    —         —    

Common stock, $0.001 par value; 200,000,000 shares authorized; 118,562,748 and 100,543,370 shares issued at December 31, 2008 and 2007, respectively

    119       101  

Additional paid-in capital

    711,195       651,038  

Accumulated other comprehensive income

    81       9  

Accumulated deficit

    (679,626 )     (581,512 )

Treasury stock, at cost; 6,607,905 and 6,263,151 shares at December 31, 2008 and 2007, respectively

    (42,134 )     (40,521 )
               

Total stockholders’ equity (deficit)

    (10,365 )     29,115  
               
  $ 171,448     $ 173,278  
               

See accompanying notes to these consolidated financial statements.

 

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LIGAND PHARMACEUTICALS INCORPORATED

CONSOLIDATED STATEMENTS OF OPERATIONS

(in thousands, except share data)

 

     Years Ended December 31,  
     2008     2007     2006  

Revenues:

      

Royalties

   $ 20,315     $ 11,409     $ —    

Collaborative research and development and other revenues

     7,000       1,485       3,977  
                        

Total revenues

     27,315       12,894       3,977  
                        

Operating costs and expenses:

      

Research and development

     30,770       44,623       41,546  

General and administrative

     23,785       30,410       43,908  

Write-off of acquired in-process research and development

     72,000       —         —    
                        

Total operating costs and expenses

     126,555       75,033       85,454  

Accretion of deferred gain on sale leaseback

     1,964       1,964       3,397  
                        

Loss from operations

     (97,276 )     (60,175 )     (78,080 )
                        

Other income (expense):

      

Interest income

     2,161       8,655       3,780  

Interest expense

     (202 )     (735 )     (2,427 )

Other, net

     (2,198 )     (1,201 )     1,331  
                        

Total other income (expense), net

     (239 )     6,719       2,684  
                        

Loss from continuing operations before income taxes

     (97,515 )     (53,456 )     (75,396 )

Income tax benefit from continuing operations

     55       18,697       18,806  
                        

Loss from continuing operations

     (97,460 )     (34,759 )     (56,590 )
                        

Discontinued operations:

      

Income (loss) from discontinued operations before income taxes

     —         5,993       (91,404 )

Gain on sale of AVINZA Product Line before income taxes

     9,584       315,184       —    

Gain (loss) on sale of Oncology Product Line before income taxes

     (10,630 )     18,037       135,778  

Income tax benefit (expense) on discontinued operations

     392       (22,767 )     (19,527 )
                        

Income (loss) from discontinued operations

     (654 )     316,447       24,847  
                        

Net income (loss)

   $ (98,114 )   $ 281,688     $ (31,743 )
                        

Basic and diluted per share amounts:

      

Loss from continuing operations

   $ (1.02 )   $ (0.35 )   $ (0.70 )

Income (loss) from discontinued operations

     (0.01 )     3.22       0.31  
                        

Net income (loss)

   $ (1.03 )   $ 2.87     $ (0.39 )
                        

Weighted average number of common shares

     95,505,421       98,124,731       80,618,528  
                        

See accompanying notes to these consolidated financial statements.

 

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LIGAND PHARMACEUTICALS INCORPORATED

CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY (DEFICIT) AND COMPREHENSIVE INCOME (LOSS)

(in thousands, except share data)

 

    Common stock   Additional
paid-in
capital
    Accumulated
other
comprehensive

income (loss)
    Accumulated
deficit
    Treasury stock     Total
stockholders’
equity
(deficit)
    Comprehensive
income (loss)
 
    Shares   Amount         Shares     Amount      

Balance at January 1, 2006

  73,136,340   $ 73   $ 720,988     $ 490     $ (831,059 )   (73,842 )   $ (911 )   $ (110,419 )  

Issuance of common stock under employee stock compensation plans

  1,268,159     2     10,820       —         —       —         —         10,822    

Issuance of common stock on conversion of debt

  25,149,005     25     154,300       —         —       —         —         154,325    

Unrealized net loss on available-for-sale securities

  —       —       —         (748 )     —       —         —         (748 )   $ (748 )

Stock-based compensation

  —       —       5,338       —         —       —         —         5,338    

Foreign currency translation adjustments

  —       —       —         (223 )     —       —         —         (223 )     (223 )

Net loss

  —       —       —         —         (31,743 )   —         —         (31,743 )     (31,743 )
                                                               

Balance at December 31, 2006

  99,553,504     100     891,446       (481 )     (862,802 )   (73,842 )     (911 )     27,352     $ (32,714 )
                       

Effect of adopting FIN 48

  —       —       —         —         (398 )   —         —         (398 )  
                                                         

Balance at January 1, 2007

  99,553,504     100     891,446       (481 )     (863,200 )   (73,842 )     (911 )     26,954    

Issuance of common stock under employee stock compensation plans

  989,866     1     4,569       —         —       —         —         4,570    

Repurchase of Company common stock

  —       —       —         —         —       (6,189,309 )     (39,610 )     (39,610 )  

Unrealized net gain on available-for-sale securities

  —       —       —         14       —       —         —         14     $ 14  

Stock-based compensation

  —       —       7,580       —         —       —         —         7,580    

Foreign currency translation adjustments

  —       —       —         476       —       —         —         476       476  

Cash dividend paid, net

  —       —       (252,557 )     —         —       —         —         (252,557 )  

Net income

  —       —       —         —         281,688     —         —         281,688       281,688  
                                                               

Balance at December 31, 2007

  100,543,370     101     651,038       9       (581,512 )   (6,263,151 )     (40,521 )     29,115     $ 282,178  
                                                               

Issuance of common stock under employee stock compensation plans

  22,339     —       130       —         —       —         —         130    

Repurchase of Company common stock

  —       —       —         —         —       (344,754 )     (1,613 )     (1,613 )  

Unrealized net gain on available-for-sale securities

  —       —       —         72       —       —         —         72     $ 72  

Stock-based compensation

  —       —       3,607       —         —       —         —         3,607    

Issuance of common stock for acquisition of Pharmacopeia

  17,997,039     18     56,420       —         —       —         —         56,438    

Net loss

  —       —       —         —         (98,114 )   —         —         (98,114 )     (98,114 )
                                                               

Balance at December 31, 2008

  118,562,748   $ 119   $ 711,195     $ 81     $ (679,626 )   (6,607,905 )   $ (42,134 )   $ (10,365 )   $ (98,042 )
                                                               

See accompanying notes to these consolidated financial statements.

 

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LIGAND PHARMACEUTICALS INCORPORATED

CONSOLIDATED STATEMENTS OF CASH FLOWS

(in thousands)

 

    Years Ended December 31,  
    2008     2007     2006  

Operating activities

     

Net income (loss)

  $ (98,114 )   $ 281,688     $ (31,743 )

Less: gain (loss) from discontinued operations

    (654 )     316,447       24,847  
                       

Loss from continuing operations

    (97,460 )     (34,759 )     (56,590 )

Adjustments to reconcile net income (loss) to net cash used in operating activities, including effects of business acquired:

     

Write-off of acquired in-process research and development

    72,000       —         —    

Gain on sale leaseback

    —         —         (3,099 )

Accretion of deferred gain on sale leaseback

    (1,964 )     (1,964 )     (298 )

Amortization of acquired technology and royalty and license rights

    —         909       12,154  

Depreciation and amortization of property and equipment

    1,052       1,706       3,227  

Amortization of debt discount and issuance costs

    —         —         836  

Loss on asset write-offs

    746       1,029       998  

Realized loss (gain) on investment

    2,038       1,300       (1,205 )

Stock-based compensation

    3,607       7,580       5,338  

Non-cash exit and restructuring costs

    5,255       —         —    

Non-cash interest expense

    —         —         561  

Other

    (16 )     487       (179 )

Changes in operating assets and liabilities, net of acquisition:

     

Accounts receivable, net

    —         11,537       9,433  

Inventories, net

    —         930       1,584  

Other current assets

    4,942       1,404       6,581  

Restricted indemnity account

    (162 )     (10,070 )     —    

Accounts payable and accrued liabilities

    (7,338 )     (54,476 )     (26,599 )

Other liabilities

    1,252       913       —    

Deferred revenue

    —         (8,657 )     —    
                       

Net cash used in operating activities of continuing operations

    (16,048 )     (82,131 )     (47,258 )

Net cash used in operating activities of discontinued operations

    (4,577 )     (15,596 )     (91,263 )
                       

Net cash used in operating activities

    (20,625 )     (97,727 )     (138,521 )

Investing activities

     

Cash acquired from acquisition of Pharmacopeia

    4,135       —         —    

Purchases of property and equipment

    (495 )     (440 )     (1,783 )

Proceeds from sale of property and equipment and building

    92       322       46,886  

Purchases of short-term investments

    (68,370 )     (25,565 )     (18,383 )

Proceeds from sale of short-term investments

    32,015       20,116       25,554  

Decrease (increase) in restricted cash and investments

    70       1,479       (1,064 )

Other, net

    71       36       73  
                       

Net cash provide by (used in) investing activities of continuing operations

    (32,482 )     (4,052 )     51,283  

Net cash provided by investing activities of discontinued operations

    8,058       347,889       145,582  
                       

Net cash provided by (used in) investing activities

    (24,424 )     343,837       196,865  

Financing activities

     

Proceeds from equipment financing arrangements

    —         —         1,030  

Principal payments on equipment financing obligations

    (1,527 )     (2,169 )     (2,537 )

Net proceeds from issuance of common stock

    130       4,387       9,050  

Dividend paid

    —         (252,742 )     —    

Dividend received on treasury stock held by company

    —         185       —    

Repurchase of common stock

    (1,613 )     (39,610 )     —    

Decrease in other long-term liabilities

    —         —         (153 )

Repayment of debt

    —         —         (11,839 )
                       

Net cash used in financing activities of continuing operations

    (3,010 )     (289,949 )     (4,449 )

Net cash provided by (used in) financing activities of discontinued operations

    —         (37,750 )     37,750  
                       

Net cash provided by (used in) financing activities

    (3,010 )     (327,699 )     33,301  
                       

Net increase (decrease) in cash and cash equivalents

    (48,059 )     (81,589 )     91,645  

Cash and cash equivalents at beginning of year

    76,812       158,401       66,756  
                       

Cash and cash equivalents at end of year

  $ 28,753     $ 76,812     $ 158,401  
                       

Supplemental disclosure of cash flow information

     

Interest paid

  $ 229     $ 1,511     $ 9,792  

Taxes paid

    140       8,371       —    

Supplemental schedule of non-cash investing and financing activities

     

Conversion of 6% convertible subordinated notes into common stock:

     

Conversion of principal amount of convertible notes

    —         —         155,250  

Conversion of unamortized debt issue costs

    —         —         (1,357 )

Conversion of unpaid accrued interest

    —         —         (454 )

Employee stock option exercises

    —         228       1,770  

Issuance of common stock for acquisition

    56,438       —         —    
                       

See accompanying notes to these consolidated financial statements.

 

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LIGAND PHARMACEUTICALS INCORPORATED

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

1. The Company and Its Business

Ligand Pharmaceuticals Incorporated, a Delaware corporation (the “Company” or “Ligand”), is a biotechnology company that focuses on drug discovery and early-stage development of pharmaceuticals that address critical unmet medical needs or that are more effective and/or safer than existing therapies, more convenient to administer and are cost effective. The consolidated financial statements include the Company’s wholly owned subsidiaries, Ligand Pharmaceuticals International, Inc., Ligand Pharmaceuticals (Canada) Incorporated, Seragen, Inc. (“Seragen”), Nexus Equity VI LLC (“Nexus”) and Pharmacopeia LLC (“Pharmacopeia”). As further discussed in Note 3, the Company acquired Pharmacopeia on December 23, 2008. As further discussed in Note 4, the Company sold its Oncology Product Line (“Oncology”) and AVINZA Product Line (“AVINZA”) on October 25, 2006 and February 26, 2007, respectively. The operating results for Oncology and AVINZA have been presented in the accompanying consolidated financial statements as “Discontinued Operations”.

The Company’s other potential products are in various stages of development. Potential products that are promising at early stages of development may not reach the market for a number of reasons. Prior to generating revenues from these products, the Company or its collaborative partners must complete the development of the products in the human health care market. No assurance can be given that: (1) product development efforts will be successful, (2) required regulatory approvals for any indication will be obtained, (3) any products, if introduced, will be capable of being produced in commercial quantities at reasonable costs or, (4) patient and physician acceptance of these products will be achieved. The Company faces risks common to companies whose products are in various stages of development. These risks include, among others, the Company’s need for additional financing to complete its research and development programs and commercialize its technologies. The Company has incurred significant losses since its inception. At December 31, 2008, the Company’s accumulated deficit was $679.6 million. Management expects that the Company will continue to incur substantial research and development expenses.

2. Significant Accounting Policies

Principles of Consolidation

The consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries. Intercompany accounts and transactions have been eliminated in consolidation.

Use of Estimates

The preparation of consolidated financial statements in conformity with generally accepted accounting principles requires the use of estimates and assumptions that affect the reported amounts of assets and liabilities, including disclosure of contingent assets and contingent liabilities, at the date of the consolidated financial statements and the reported amounts of revenues and expenses, in-process research and development, goodwill, deferred revenues and income tax net operating losses during the reporting period. The Company’s critical accounting policies are those that are both most important to the Company’s consolidated financial condition and results of operations and require the most difficult, subjective or complex judgments on the part of management in their application, often as a result of the need to make estimates about the effect of matters that are inherently uncertain. Because of the uncertainty of factors surrounding the estimates or judgments used in the preparation of the consolidated financial statements, actual results may materially vary from these estimates.

Cash, Cash Equivalents and Short-term Investments

Cash and cash equivalents consist of cash and highly liquid securities with maturities at the date of acquisition of three months or less. Non-restricted equity and debt security investments with a maturity of more

 

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than three months are considered short-term investments and have been classified by management as available-for-sale. Such investments are carried at fair value, with unrealized gains and losses included as a separate component of stockholders’ equity. The Company determines the cost of investments based on the specific identification method.

Restricted Cash and Investments

Restricted cash and investments consist of certificates of deposit held with a financial institution as collateral under equipment financing and third-party service provider arrangements. The certificates of deposit have been classified by management as held-to-maturity and are accounted for at amortized cost.

Concentrations of Credit Risk

Financial instruments that potentially subject the Company to significant concentrations of credit risk consist primarily of cash equivalents and investments.

The Company invests its excess cash principally in United States government debt securities, investment grade corporate debt securities and certificates of deposit. The Company has established guidelines relative to diversification and maturities that maintain safety and liquidity. These guidelines are periodically reviewed and modified to take advantage of trends in yields and interest rates. Except as described in Note 5, the Company has not experienced any significant losses on its cash equivalents, short-term investments or restricted investments.

Property and Equipment

Property and equipment is stated at cost and consists of the following (in thousands):

 

     December 31,  
     2008     2007  

Equipment and leasehold improvements

   $ 54,664     $ 40,577  

Less accumulated depreciation and amortization

     (41,761 )     (37,712 )
                
   $ 12,903     $ 2,865  
                

Depreciation of equipment is computed using the straight-line method over the estimated useful lives of the assets which range from three to ten years. Leasehold improvements are amortized using the straight-line method over their estimated useful lives or their related lease term, whichever is shorter.

Goodwill

Goodwill represents the excess purchase price of net tangible and intangible assets acquired in business combinations over their estimated fair value. In accordance with Statement of Financial Accounting Standards No. 141, “Business Combinations” (SFAS 141) and Statement of Financial Accounting Standards No. 142, “Goodwill and Other Intangible Assets” (SFAS 142), goodwill is tested for impairment on an annual basis and earlier if there is an indicator of impairment. Furthermore, SFAS 142 requires purchased intangible assets other than goodwill to be amortized over their useful lives unless these lives are determined to be indefinite.

Management expects to perform its goodwill impairment test annually and whenever an event or circumstance indicates that impairment has occurred.

Other Intangible Assets

Intangible assets are amortized using the straight-line method over their estimated useful lives. There was no amortization expense related to other intangibles assets recorded for the year ended December 31, 2008.

 

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Acquired in-process research and development

For acquisitions prior to January 1, 2009, the estimated fair value of acquired in-process R&D (“IPR&D”) projects, which have not reached technological feasibility at the date of acquisition and which do not have an alternative future use, are immediately expensed. In 2008, the Company wrote off $72.0 million of acquired IPR&D related to the acquisition of Pharmacopeia, Inc.

Impairment of Long-Lived Assets

Management reviews long-lived assets for impairment annually or whenever events or changes in circumstances indicate the carrying amount of an asset may not be recoverable. Recoverability of assets to be held and used is measured by a comparison of the carrying amount of an asset to future undiscounted net cash flows expected to be generated by the asset. If such assets are considered to be impaired, the impairment to be recognized is measured as the amount by which the carrying amount of the assets exceeds the fair value of the assets. Fair value for the Company’s long-lived assets is determined using the expected cash flows discounted at a rate commensurate with the risk involved. In 2006, the Company recorded an impairment charge of $1.0 million to reflect the discontinuation of certain operational software. In 2007, the Company recorded an impairment charge of $1.0 million to reflect the abandonment or disposal of certain equipment items that are no longer used in the Company’s ongoing operations following the sale of the Company’s AVINZA product line and the reduction in workforce. As of December 31, 2008, management believes that the future undiscounted cash flows to be received from its long-lived assets will exceed the assets’ carrying value.

Fair Value of Financial Instruments

In September 2006, the Financial Accounting Standards Board (FASB) issued SFAS No. 157, “Fair Value Measurements” (SFAS 157). SFAS 157 establishes a framework for measuring fair value in accordance with generally accepted accounting principles and expands disclosures about fair value measurements. The statement defines fair value as the exit price that would be received to sell an asset or paid to transfer a liability. Fair value is a market-based measurement that should be determined using assumptions that market participants would use in pricing an asset or liability. The statement establishes a three-level hierarchy to prioritize the inputs used in measuring fair value. The levels are described in the table below with Level 1 having the highest priority and Level 3 having the lowest.

In February 2008, the FASB issued FASB Staff Position (FSP) 157-b which delayed the effective date of SFAS 157 for one year for all nonfinancial assets and nonfinancial liabilities, except those that are recognized or disclosed at fair value in the financial statements on a recurring basis (at least annually). SFAS 157 and FSP 157-b are effective for financial statements issued for fiscal years beginning after November 15, 2007. Management has elected a partial deferral of Statement 157 under the provisions of FSP 157-b and, effective January 1, 2008, the Company adopted SFAS 157 for those assets and liabilities that are remeasured at fair value on a recurring basis. This partial adoption of SFAS 157 did not have a material effect on the Company’s consolidated financial statements as of and for the year ended December 31, 2008.

 

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The following table provides a summary of the assets and liabilities that are measured at fair value on a recurring basis as of December 31, 2008:

 

Fair Value Measurements at Reporting Date Using

     Total    Quoted Prices in Active
Markets for Identical
Assets
   Significant Other
Observable Inputs
   Significant
Unobservable
Inputs
      (Level 1)    (Level 2)    (Level 3)

Assets:

           

Fixed income available-for-sale securities

   $ 51,918    $ 50,255    $ 1,663    $ —  
                           

Total assets

   $ 51,918    $ 50,255    $ 1,663    $ —  
                           

Liabilities:

           

Warrant liability

   $ 670    $ —      $ —      $ 670
                           

Total liabilities

   $ 670    $ —      $ —      $ 670
                           

The Company’s short-term investments are fixed income available-for-sale securities and include U.S. Government Notes and Corporate Discount Commercial Paper. The fair value of the Company’s short-term investments are determined using quoted market prices in active markets. The fair value of the warrant liability is determined using the Black-Scholes option-pricing model, which uses certain significant observable inputs, including stock price (quoted market prices in active market), warrant exercise price (defined in warrant agreement), expected life of warrant (defined in warrant agreement), dividend yields (determined by the Company), and risk-free interest rate (quoted market prices based on expected life assumption).

Revenue Recognition

Royalties on sales of AVINZA and PROMACTA are recognized in the quarter reported by the respective partner.

Revenue from research funding under the Company’s collaboration agreements is earned and recognized on a percentage of completion basis as research hours are incurred in accordance with the provisions of each agreement.

Revenue earned related to up-front product and technology license fees is recognized in accordance with Staff Accounting Bulletin (SAB) 104 issued by the Securities and Exchange Commission (SEC), Emerging Issue Task Force (EITF) No. 00-21, “Revenue Arrangements with Multiple Deliverables” (EITF 00-21), EITF No. 07-1, “Accounting for Collaborative Arrangements” (EITF 07-1) and EITF No. 07-3, “Accounting for Nonrefundable Advance Payments for Goods or Services Received for Use in Future Research and Development Activities” (EITF 07-3) issued by the FASB. Accordingly, amounts received under multiple-element arrangements requiring ongoing services or performance by the Company are recognized over the period of such services or performance.

Revenue from milestones is recognized when earned, as evidenced by written acknowledgement from the collaborator, provided that (i) the milestone event is substantive, its achievability was not reasonably assured at the inception of the agreement, and the Company has no further performance obligations relating to that event, and (ii) collectibility is reasonably assured. If these criteria are not met, the milestone payment is recognized over the remaining period of the Company’s performance obligations under the arrangement.

The composition of collaborative research and development and other revenues is as follows (in thousands):

 

     Year Ended December 31,
     2008    2007    2006

Collaborative research and development

   $ —      $ —      $ 1,678

License fees

     5,000      —        —  

Development milestones and other

     2,000      1,485      2,299
                    
   $ 7,000    $ 1,485    $ 3,977
                    

 

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Preclinical Study and Clinical Trial Accruals

Substantial portions of the Company’s preclinical studies and all of the Company’s clinical trials have been performed by third-party laboratories, contract research organizations, or other vendors (collectively CROs). Some CROs bill monthly for services performed, while others bill based upon milestone achievement. The Company accrues for each of the significant agreements it has with CROs on a monthly basis. For preclinical studies, accruals are estimated based upon the percentage of work completed and the contract milestones achieved. For clinical studies, accruals are estimated based upon a percentage of work completed, the number of patients enrolled and the duration of the study. The Company monitors patient enrollment, the progress of clinical studies and related activities to the extent possible through internal reviews of data reported to it by the CROs, correspondence with the CROs and clinical site visits. The Company’s estimates are dependent upon the timelines and accuracy of the data provided by its CROs regarding the status of each program and total program spending. The Company periodically evaluates its estimates to determine if adjustments are necessary or appropriate based on information it receives concerning changing circumstances, and conditions or events that may affect such estimates. No material adjustments to preclinical study and clinical trial accrued expenses have been recognized to date.

Warrant Liability

The Company, in accounting for its warrants, follows EITF No. 00-19, “Accounting for Derivative Financial Instruments Indexed to, and Potentially Settled in, a Company’s Own Stock” (EITF 00-19), which provides guidance for distinguishing between permanent equity, temporary equity and assets and liabilities. Under EITF 00-19, to qualify as permanent equity, an equity derivative, including warrants, must permit the Company to settle in unregistered shares. Under securities law, if the warrants were issued in connection with a public offering and have a cash settlement feature at the holder’s option, the Company does not have the ability to settle in unregistered shares. Therefore, the warrants cannot be classified as permanent equity and are instead classified as a liability. The warrants that the Company issued as part of its equity financing in October 2006 meet this criteria, and their fair value has been recorded as a liability in the accompanying balance sheets. Other warrants the Company had previously issued qualify as permanent equity and do not require remeasurement.

The Company records its warrant liabilities at fair value using a Black-Scholes option-pricing model and remeasures at each reporting date until the warrants are exercised or have expired. Changes in the fair value of the warrants are reported in the statements of operations as income or expense. The fair value of the warrants is subject to significant fluctuation based on changes in the Company’s stock price, expected volatility, expected life, the risk-free interest rate and dividend yield. The market price for the Company’s common stock has been and may continue to be volatile. Consequently, future fluctuations in the price of the Company’s common stock may cause significant increases or decreases in the fair value of the warrants.

Assets and Liabilities Related to Discontinued Operations

Medicaid Rebates

The Company’s products related to the commercial operations that were sold were subject to state government-managed Medicaid programs whereby discounts and rebates are provided to participating state governments. The Company is still obligated to pay for these rebates for products in the distribution channel that were not sold-through at the time of the sale of the Company’s commercial operations. Medicaid rebates are accounted for by establishing an accrual in an amount equal to the Company’s estimate of Medicaid rebate claims attributable to sales recognized in that period. The estimate of the Medicaid rebates accrual is determined primarily based on historical experience regarding Medicaid rebates, as well as current and historical prescription activity provided by external sources, current contract prices and any expected contract changes. Management additionally considers any legal interpretations of the applicable laws related to Medicaid and qualifying federal

 

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and state government programs and any new information regarding changes in the Medicaid programs’ regulations and guidelines that would impact the amount of the rebates. Management adjusts the accrual periodically throughout each period to reflect actual experience, expected changes in future prescription volumes and any changes in business circumstances or trends.

Government Chargebacks

The Company’s products related to the commercial operations that were sold were subject to certain programs with federal government entities and other parties whereby pricing on products is extended below wholesaler list price to participating entities. The Company is still obligated to pay for these chargebacks for products in the distribution channel that were not sold-through at the time of the sale of the Company’s commercial operations. These entities purchase products through wholesalers at the lower vendor price, and the wholesalers charge the difference between their acquisition cost and the lower vendor price back to the Company. Chargebacks are accounted for by establishing an accrual in an amount equal to the estimate of chargeback claims. Management determines estimates of the chargebacks primarily based on historical experience regarding chargebacks and current contract prices under the vendor programs. Management considers vendor payments and claim processing time lags and adjusts the accrual periodically throughout each period to reflect actual experience and any changes in business circumstances or trends.

Managed Health Care Rebates and Other Contract Discounts

The Company previously offered rebates and discounts on certain products related to the commercial operations that were sold to managed health care organizations and to other contract counterparties such as hospitals and group purchasing organizations in the U.S. The Company is still obligated to pay for these rebates and discounts for products in the distribution channel that were not sold-through at the time of the sale of the Company’s commercial operations. Managed health care rebates and other contract discounts are accounted for by establishing an accrual in an amount equal to the estimate of managed health care rebates and other contract discounts. Estimates of the managed health care rebates and other contract discounts accruals are determined primarily based on historical experience regarding these rebates and discounts and current contract prices. Management also considers the current and historical prescription activity provided by external sources, current contract prices and any expected contract changes and adjusts the accrual periodically throughout each period to reflect actual experience and any changes in business circumstances or trends.

Product Returns

In connection with the sale of the Company’s product lines, the Company retained the obligation for returns of product that were shipped to wholesalers prior to the close of the transactions. The accruals for product returns, which were recorded as part of the accounting for the sales transactions, are based on historical experience. Any subsequent changes to the Company’s estimate of product returns are accounted for as a component of discontinued operations.

Costs and Expenses

Collaborative research and development expense consists of the labor, material, equipment and allocated facilities cost of the Company’s scientific staff who are working pursuant to the Company’s collaborative agreements. From time to time, collaborative research and development expense includes costs related to research efforts in excess of those required under certain collaborative agreements. Management has the discretion to set the scope of such excess efforts and may increase or decrease the level of such efforts depending on the Company’s strategic priorities.

Proprietary research and development expense consists of intellectual property in-licensing costs, labor, materials, contracted services, and allocated facility costs that are incurred in connection with internally funded drug discovery and development programs.

 

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Research and development costs are expensed as incurred. Research and development expenses from continuing operations were $30.8 million, $44.6 million, and $41.5 million in 2008, 2007, and 2006, respectively, of which 100%, 100%, and 95%, respectively, were sponsored by Ligand, and the remainder of which was funded pursuant to collaborative research and development arrangements.

Income Taxes

The Company recognizes liabilities or assets for the deferred tax consequences of temporary differences between the tax bases of assets or liabilities and their reported amounts in the financial statements in accordance with SFAS No. 109, Accounting for Income Taxes (SFAS 109). These temporary differences will result in taxable or deductible amounts in future years when the reported amounts of the assets or liabilities are recovered or settled. SFAS 109 requires that a valuation allowance be established when management determines that it is more likely than not that all or a portion of a deferred tax asset will not be realized. Management evaluates the realizability of its net deferred tax assets on a quarterly basis and valuation allowances are provided, as necessary. During this evaluation, management reviews its forecasts of income in conjunction with other positive and negative evidence surrounding the realizability of its deferred tax assets to determine if a valuation allowance is required. Adjustments to the valuation allowance will increase or decrease the Company’s income tax provision or benefit. Management also applies the guidance of SFAS 109 to determine the amount of income tax expense or benefit to be allocated among continuing operations, discontinued operations, and items charged or credited directly to stockholders’ equity (deficit).

Due to the adoption of SFAS No. 123R, “Share-Based Payment” (SFAS 123R) beginning January 1, 2006, the Company recognizes windfall tax benefits associated with the exercise of stock options directly to stockholders’ equity only when realized. Accordingly, deferred tax assets are not recognized for net operating loss carryforwards resulting from windfall tax benefits occurring from January 1, 2006 onward. A windfall tax benefit occurs when the actual tax benefit realized by the Company upon an employee’s disposition of a share-based award exceeds the deferred tax asset, if any, associated with the award that the Company had recorded.

The Company adopted the provisions of FASB Interpretation No. 48 (FIN 48), “Accounting for Uncertainty in Income Taxes”, on January 1, 2007. FIN 48 clarifies the accounting for income taxes by prescribing a minimum probability threshold that a tax position must meet before a financial statement benefit is recognized. The minimum threshold is defined in FIN 48 as a tax position that is more likely than not to be sustained upon examination by the applicable taxing authority, including resolution of any related appeals or litigation processes, based on the technical merits of the position. The Company recognizes interest and penalties related to uncertain tax positions in income tax expense.

Income (Loss) Per Share

Net income (loss) per share is computed using the weighted average number of common shares outstanding. Basic and diluted income (loss) per share amounts are equivalent for the periods presented as the inclusion of potential common shares in the number of shares used for the diluted computation would be anti-dilutive to loss per share from continuing operations. In accordance with SFAS No. 128, “Earnings Per Share”, no potential common shares are included in the computation of any diluted per share amounts, including income (loss) per share from discontinued operations, as the Company reported a net loss from continuing operations for all periods presented. Potential common shares, the shares that would be issued upon the conversion of convertible notes, the exercise of outstanding warrants and stock options, and the vesting of restricted shares, were 4.5 million, 2.2 million, and 5.8 million at December 31, 2008, 2007, and 2006, respectively.

Accounting for Stock-Based Compensation

The Company has employee compensation plans under which various types of stock-based instruments are granted. The Company accounts for its share-based payments in accordance with SFAS 123R. This statement

 

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requires all share-based payments to employees, including grants of employee stock options, to be recognized in the Consolidated Statements of Operations as compensation expense (based on their estimated fair values) generally over the vesting period of the awards using the straight-line method.

Additionally, the Company accounts for the fair value of options granted to non-employee consultants under Emerging Issues Task Force EITF 96-18, “Accounting for Equity Instruments That Are Issued to Other Than Employees for Acquiring, or in Conjunction with Selling, Goods or Services.”

Employee Stock Purchase Plan

The Company also has an employee stock purchase plan (the “2002 ESPP”). The 2002 ESPP was originally adopted July 1, 2001 and amended through June 30, 2003 to allow employees to purchase a limited amount of common stock at the end of each three month period at a price equal to the lesser of 85% of fair market value on a) the first trading day of the period, or b) the last trading day of the Lookback period (the “Lookback Provision”). The 15% discount and the Lookback Provision make the 2002 ESPP compensatory under SFAS 123R. There were 46,217, 29,139 and 24,763 shares of common stock issued under the 2002 ESPP in 2008, 2007 and 2006, respectively, resulting in an expense of $0.03 million, $0.04 million and $0.1 million, respectively. For shares purchased under the Company’s employee stock purchase plan (ESPP), a weighted-average expected volatility of 60%, 38%, and 50% was used for 2008, 2007 and 2006, respectively. The expected term for shares issued under the ESPP is three months. As of December 31, 2008, 462,857 shares of common stock had been issued under the 2002 ESPP to employees and 47,391 shares are available for future issuance.

Foreign Currency Translation

The Company’s foreign subsidiaries maintain their accounts in their functional currency. The functional currency financial statements are translated into U.S. dollars in accordance with SFAS 52. Assets and liabilities of foreign operations are translated using period-end exchange rates. Revenues and expenses are translated using average exchange rates during each period. Translation gains and losses are classified as a component of stockholders’ equity (deficit). Transaction gains and losses resulting from the settlement of assets and liabilities in a currency other than the functional currency are charged to the Statement of Operations.

Comprehensive Income (Loss)

Comprehensive income (loss) represents net income (loss) adjusted for the change during the periods presented in unrealized gains and losses on available-for-sale securities less reclassification adjustments for realized gains or losses included in net income (loss), as well as foreign currency translation adjustments for the 2007 and 2006 periods. The accumulated unrealized gains or losses and cumulative foreign currency translation adjustments are reported as accumulated other comprehensive income (loss) as a separate component of stockholders’ equity.

Segment Reporting

The Company currently operates in a single operating segment. The Company generates revenue from various sources that result primarily from its underlying research and development activities. In addition, financial results are prepared and reviewed by management as a single operating segment. Management continually evaluates the benefits of operating in distinct segments and will report accordingly when such distinction is made.

Guarantees and Indemnifications

The Company accounts for and discloses guarantees in accordance with FASB Interpretation No. 45 (FIN 45), “Guarantor’s Accounting and Disclosure Requirements for Guarantees Including Indirect Guarantees of

 

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Indebtedness of Others, an interpretation of FASB Statements No. 5, 57 and 107 and rescission of FIN 34.” The following is a summary of the Company’s agreements that the Company has determined are within the scope of FIN 45:

Under its bylaws, the Company has agreed to indemnify its officers and directors for certain events or occurrences arising as a result of the officer’s or director’s serving in such capacity. The term of the indemnification period is for the officer’s or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited. The Company has a directors and officers liability insurance policy that limits its exposure and enables it to recover a portion of any future amounts paid. These insurance policies, however, do not cover the ongoing legal costs or the fines, if any, that may become due in connection with the ongoing SEC investigation of the Company, following the use of prior directors and officers liability insurance policy limits to settle certain shareholder litigation matters (see discussion of SEC investigation at Note 9). The SEC investigation is ongoing, and management is currently unable to assess the duration, extent, and cost of such investigation. Further, management is unable to assess the amount of such costs that may in turn be required to be reimbursed to any individual director or officer under the Company’s indemnification agreements as the scope of the investigation cannot be apportioned amongst the Company and the indemnified officers and directors. Accordingly, a liability has not been recorded for the fair value of the ongoing and ultimate obligations, if any, related to the SEC investigation.

Reclassifications

Certain reclassifications have been made to the 2007 and 2006 financial statements to conform to the 2008 presentation.

New Accounting Pronouncements

In September 2006, the FASB issued SFAS No. 157, “Fair Value Measurements” (SFAS 157). SFAS 157 defines fair value, establishes a framework for measuring fair value under GAAP, and expands disclosures about fair value measurements. SFAS 157 does not require any new fair value measurements but rather eliminates inconsistencies in guidance found in various prior accounting pronouncements and is effective for financial statements issued for fiscal years beginning after November 15, 2007. In February 2008, the FASB issued FASB FSP 157-2 which delays the effective date of SFAS 157 for all nonfinancial assets and nonfinancial liabilities, except those that are recognized or disclosed at fair value in the financial statements on a recurring basis (at least annually), until fiscal years beginning after November 15, 2008, and interim periods within those fiscal years. These nonfinancial items include assets and liabilities such as reporting units measured at fair value in a goodwill impairment test and nonfinancial assets acquired and liabilities assumed in a business combination. Effective January 1, 2008, the Company adopted SFAS 157 for financial assets and liabilities recognized at fair value on a recurring basis. The adoption of SFAS 157 did not have a material impact on the Company’s consolidated results of operations or financial position.

In December 2007, the FASB issued SFAS No. 141 (revised 2007), “Business Combinations” (SFAS 141R). SFAS 141R requires an acquirer to (i) recognize the assets acquired, liabilities assumed, contractual contingencies, and contingent consideration at fair value at the acquisition date, (ii) recognize acquisition-related costs separately from the acquisition, (iii) to recognize “negative goodwill” in earnings as a gain attributable to the acquisition, and (iv) to recognize changes in the amount of its deferred tax benefits that are recognizable because of the business combination either in earnings in the period of the combination or directly in contributed capital, depending on the circumstances. SFAS 141R is effective for business combinations for which the acquisition date is on or after the beginning of the first annual reporting period beginning on or after December 15, 2008. Management is evaluating the impact, if any, that SFAS 141R may have on its consolidated results of operations and financial position.

In December 2007, the FASB issued Statement No. 160, “Noncontrolling Interests in Consolidated Financial Statements—an amendment of ARB No. 51” (SFAS 160). SFAS 160 requires entities to present ownership interests in subsidiaries held by parties other than the parent entity within the equity section of the

 

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consolidated balance sheet, to present the amount of consolidated net income attributable to the parent and to the noncontrolling interest in the consolidated statement of operations, to recognize any changes in ownership interests as equity transactions, and to measure at fair value any retained noncontrolling equity investment upon deconsolidation of a subsidiary. The Company will adopt SFAS 160 in the first interim period of fiscal 2009, and management does not believe that the adoption of this statement will have a material impact on its consolidated results of operations and financial position.

In March 2008, the FASB issued Statement No. 161, “Disclosures about Derivative Instruments and Hedging Activities—an amendment of FASB Statement No. 133” (SFAS 161). SFAS 161 requires entities to disclose the objectives for using derivative instruments in terms of underlying risk and accounting designation, to disclose the fair values of derivative instruments and their gains and losses in a tabular format, and to disclose information about credit-risk-related contingent features. The Company will adopt SFAS 161 in the first interim period of fiscal 2009, and management does not believe that the adoption of this statement will have a material impact on its consolidated results of operations and financial position.

3. Acquisition of Pharmacopeia

On December 23, 2008, the Company completed the acquisition of Pharmacopeia, Inc., a clinical development stage biopharmaceutical company dedicated to discovering and developing novel small molecule therapeutics to address significant medical needs, under which the Company acquired all outstanding shares of Pharmacopeia in a cash and stock transaction. The acquisition was accounted for as a business combination. In connection with the acquisition, the Company issued 17,997,039 shares of common stock to Pharmacopeia stockholders, or 0.5985 shares for each outstanding Pharmacopeia share, as well as $9.3 million in cash. The value of the common stock issued was derived from the number of Ligand common shares issued at a price of $3.14 per share determined by the average closing price of Ligand shares for the two days prior, the day of, and the two days subsequent to the public announcement on September 24, 2008. In addition, Pharmacopeia security holders received a contingent value right (CVR) that entitles each holder the right to receive a proportionate share of an aggregate of $15.0 million if Ligand enters into a license, sale, development, marketing or option agreement with respect to any product candidate from Pharmacopeia’s DARA program (other than any agreement with Bristol-Meyers Squibb or any of its affiliates) on or prior to December 31, 2011. The estimated fair value of the CVRs is not included in the total purchase price as the Company’s management has deemed, based on currently available information, that the likelihood of payment is not probable. The results of Pharmacopeia’s operations have been included in the consolidated financial statements commencing December 23, 2008.

The components of the preliminary purchase price allocation for Pharmacopeia are as follows:

 

Purchase Consideration:

  

(in thousands)

  

Fair value of common stock issued to Pharmacopeia shareholders

   $ 56,439

Cash paid to Pharmacopeia shareholders

     9,337

Transaction costs

     4,344
      

Total purchase consideration

   $ 70,120
      

 

Allocation of Purchase Price:

  

(in thousands)

  

Cash acquired

   $ 17,754  

Other current assets

     1,390  

Property and equipment

     11,500  

Acquired intangible assets

     2,000  

In-process research and development

     72,000  

Goodwill

     3,375  

Other assets

     144  

Liabilities assumed

     (38,043 )
        
   $ 70,120  
        

 

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The acquired identified intangible assets with definite lives from the acquisition with Pharmacopeia are as follows:

 

Acquired Intangible Assets

  

(in thousands)

  

Collaborative research and development with Schering-Plough

   $ 2,000

The weighted-average amortization period for the collaborative research and development with Schering Plough is 3 years.

The Company has allocated $72.0 million of the purchase price of Pharmacopeia to acquired In-Process Research and Development (IPR&D). This amount represents the estimated fair value of various acquired in-process projects that have not yet reached technological feasibility and do not have future alternative use as of the date of the merger. The amount is related to internal and partnered product candidates targeting a variety of indications and currently in various stages of development ranging from preclinical to Phase II. Of the total amount, $29.0 million relates to product candidates currently in the preclinical stage of development, $9.0 million relates to product candidates currently in Phase I clinical trials and $34.0 million relates to product candidates currently in Phase II clinical trials.

Management used the “income method” to determine the estimated fair values of acquired IPR&D, which uses a discounted cash flow model and applies a probability weighting based on estimates of successful product development and commercialization to estimated future net cash flows resulting from projected revenues and related costs. These success rates take into account the stages of completion and the risks surrounding successful development and commercialization of the underlying product candidates. These cash flows were then discounted to present value using a discount rate of 40% for product candidates in the preclinical stage, 35% for product candidates currently in Phase I clinical trials and 30% for product candidates currently in Phase II clinical trials.

Had the merger with Pharmacopeia been completed as of the beginning of 2007, the Company’s pro forma results for 2008 and 2007 would have been as follows:

 

(in thousands, except per share data)    2008     2007  

Revenue

   $ 51,351     $ 34,300  

Operating (loss)

     (151,503 )     (185,435 )

Net income (loss)

     (145,220 )     142,190  

Basic and diluted earnings per share:

    

Continuing operations

   $ (1.27 )   $ (1.50 )

Discontinued operations

   $ (0.01 )   $ 2.73  

Net income (loss)

   $ (1.28 )   $ 1.22  

Basic and diluted weighted average shares

     113,060       116,122  

The primary adjustments relate to the purchase accounting impact of the write-off of IPR&D and the amortization of the acquired collaborative research and development collaboration with Schering-Plough. The above pro forma information was determined based on historical GAAP results adjusted for the purchase price allocation and estimated related changes in income associated with the merger of Pharmacopeia.

 

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4. Discontinued Operations

Oncology Product Line

On September 7, 2006, the Company, Eisai Inc., a Delaware corporation and Eisai Co., Ltd., a Japanese company (together with Eisai Inc., “Eisai”), entered into a purchase agreement (the “Oncology Purchase Agreement”) pursuant to which Eisai agreed to acquire all of the Company’s worldwide rights in and to the Company’s oncology products, including, among other things, all related inventory, equipment, records and intellectual property, and assume certain liabilities as set forth in the Oncology Purchase Agreement. The Oncology Product Line included the Company’s four marketed oncology drugs: ONTAK, Targretin capsules, Targretin gel and Panretin gel. Pursuant to the Oncology Purchase Agreement, at closing on October 25, 2006, Ligand received $185.0 million in net cash proceeds, net of $20.0 million that was funded into an escrow account to support any potential indemnification claims made by Eisai following the closing of the sale as further discussed below. The Company also incurred $1.7 million in transaction fees and costs associated with the sale that are not reflected in net cash proceeds. The Company recorded a pre-tax gain on the sale of $135.8 million in the fourth quarter of 2006. In 2007, the Company recognized a $20.8 million pre-tax gain resulting from the release of funds from the escrow account partially offset by a $2.8 million pre-tax loss due to subsequent changes in certain estimates of assets and liabilities recorded as of the sale date. In 2008, the Company recognized a $10.6 million pre-tax loss resulting from the settlement of litigation for $13.0 million partially offset by a $2.4 million pre-tax gain due to subsequent changes in certain estimates of assets and liabilities recorded as of the sale date.

Additionally, $38.6 million of the proceeds received from Eisai were deposited into an escrow account to repay a loan received from King Pharmaceuticals, Inc. (“King”), the proceeds of which were used to pay the Company’s co-promote termination obligation to Organon in October 2006. The escrow amounts were released and the loan repaid to King in January 2007.

In connection with the Oncology Purchase Agreement with Eisai, the Company entered into a transition services agreement whereby the Company agreed to perform certain transition services for Eisai, in order to effect, as rapidly as practicable, the transition of purchased assets from Ligand to Eisai. In exchange for these services, Eisai paid the Company a monthly service fee through June 25, 2007. Fees earned under the transition services agreement during 2007 and 2006, which were recorded as an offset to operating expenses, were $2.7 million and $1.9 million, respectively.

The Company agreed to indemnify Eisai, after the closing, for damages suffered by Eisai arising from any breach of any of the Company’s representations, warranties, covenants or obligations in the Oncology Purchase Agreement. The Company’s obligation to indemnify Eisai extends beyond the closing up to, in some cases, 18 months or 36 months and, in other cases, until the expiration of the applicable statute of limitations. In a few instances, the Company’s obligation to indemnify Eisai survives in perpetuity. The Company’s agreement with Eisai required that $20.0 million of the total upfront cash payment be deposited into an escrow account to secure the Company’s indemnification obligations to Eisai after the closing. Of the escrowed amount, $10.0 million was released to the Company on April 25, 2007, and the remaining $10.0 million, plus interest of $0.8 million, was released to the Company on October 25, 2007. The Company’s liability for any indemnification claim brought by Eisai is generally limited to $30.0 million. However, the Company’s obligation to provide indemnification on certain matters is not subject to these indemnification limits. For example, the Company agreed to retain, and provide indemnification without limitation to Eisai for, all liabilities related to certain claims regarding promotional materials for the ONTAK and Targretin drug products. Management cannot estimate the liabilities that may arise as a result of these matters and, therefore, no accrual has been recorded at December 31, 2008 and 2007.

Prior to the Oncology sale, the Company recorded accruals for rebates, chargebacks, and other discounts related to Oncology products when product sales were recognized as revenue under the sell-through method. Upon the Oncology sale, the Company accrued for rebates, chargebacks, and other discounts related to Oncology

 

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products in the distribution channel which had not sold-through at the time of the Oncology sale and for which the Company retained the liability subsequent to the sale. These products expired at various dates through July 31, 2008. The Company’s accruals for Oncology rebates, chargebacks, and other discounts total $0.4 million and $1.2 million as of December 31, 2008 and 2007, respectively, and are included in accrued liabilities in the accompanying consolidated balance sheets.

Additionally, and pursuant to the terms of the Oncology Purchase Agreement, the Company retained the liability for returns of product from wholesalers that had been sold by the Company prior to the close of the transaction. Accordingly, as part of the accounting for the gain on the sale of the Oncology Product Line, the Company recorded a reserve for Oncology product returns. Under the sell-through revenue recognition method, the Company previously did not record a reserve for returns from wholesalers. Oncology products sold by the Company may be returned through a specified period subsequent to the product expiration date, but no later than July 31, 2009. The Company’s reserve for Oncology returns is $0.9 million and $4.4 million as of December 31, 2008 and 2007, respectively, and is included in accrued liabilities in the accompanying consolidated balance sheets.

AVINZA Product Line

On September 6, 2006, Ligand and King Pharmaceuticals, Inc. (King), entered into a purchase agreement (the “AVINZA Purchase Agreement”), pursuant to which King agreed to acquire all of the Company’s rights in and to AVINZA in the United States, its territories and Canada, including, among other things, all AVINZA inventory, records and related intellectual property, and assume certain liabilities as set forth in the AVINZA Purchase Agreement (collectively, the “Transaction”). In addition, King, subject to the terms and conditions of the AVINZA Purchase Agreement, agreed to offer employment following the closing of the Transaction (the “Closing”) to certain of the Company’s existing AVINZA sales representatives or otherwise reimburse the Company for agreed upon severance arrangements offered to any such non-hired representatives.

Pursuant to the AVINZA Purchase Agreement, at Closing on February 26, 2007 (the “Closing Date”), the Company received $280.4 million in net cash proceeds, which is net of $15.0 million that was funded into an escrow account to support any potential indemnification claims made by King following the Closing. The purchase price reflected a reduction of $12.7 million due to the preliminary estimate of retail inventory levels of AVINZA at the Closing Date exceeding targeted levels. After final studies and review by King, the final retail inventory-level adjustment was determined to be $11.2 million. The Company received the additional $1.5 million in proceeds in April 2007. The purchase price also reflects a reduction of $6.0 million for anticipated higher cost of goods for King related to the Catalent Pharma Solutions (formerly Cardinal Health PTS, LLC), or Catalent, manufacturing and packaging agreement. At the closing, Ligand agreed to not assign the Catalent agreement to King, wind down the contract, and remain responsible for any resulting liabilities. Subsequent to the closing, on April 30, 2007, the Company entered into a letter agreement with Catalent which terminated, without penalty to either party, the manufacturing and packaging agreement and certain related quality agreements with Catalent. In connection with the termination, the Company and Catalent agreed that certain provisions of the manufacturing and packaging agreement would survive and Catalent would continue to perform limited services. Catalent will also continue to manufacture LGD-4665 capsules for the Company under the terms of a separate agreement. The letter agreement with Catalent also contained a mutual general release of all claims arising from or related to the manufacturing and packaging agreement. The Company paid $0.3 million to a former Ligand executive in connection with the negotiation of the termination of the Catalent manufacturing and packaging agreement.

 

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The net cash received also includes reimbursement of $47.8 million for co-promote termination payments which had previously been paid to Organon, $0.9 million of interest Ligand paid King on a loan that was repaid in January 2007 and $0.5 million of severance expense for AVINZA sales representatives not offered positions with King. A summary of the net cash proceeds received, exclusive of $6.6 million in transaction costs and adjusted to reflect the final results of the retail inventory study, is as follows (in thousands):

 

Purchase price

   $  265,000  

Reimbursement of Organon payments

     47,750  

Repayment of interest on King loan

     883  

Reimbursement of sales representative severance costs

     453  
        
     314,086  

Less retail pharmacy inventory adjustment

     (11,225 )

Less cost of goods manufacturing adjustment

     (6,000 )
        

Net cash proceeds

   $ 296,861  
        

King also assumed Ligand’s co-promote termination obligation to make payments to Organon based on net sales of AVINZA ($58.5 million and $59.5 million as of December 31, 2008 and 2007, respectively). As Organon has not consented to the legal assignment of the co-promote termination obligation from Ligand to King, Ligand remains liable to Organon in the event of King’s default of this obligation. The Company also incurred $6.6 million in transaction fees and other costs associated with the sale that are not reflected in the net cash proceeds, of which $3.6 million was recognized in 2006. The Company recognized $3.6 million in the first quarter of 2007 for investment banking services and related expenses. The Company disputed the amount of the fees owed to the investment banking firm and as a result, the parties agreed to settle the matter for $3.0 million, which was paid in June 2007. The Company recorded a pre-tax gain on the sale of $310.1 million in the first quarter of 2007. The Company recorded an additional $0.3 million pre-tax gain on the sale in the second quarter of 2007 due to subsequent changes in certain estimates of assets and liabilities recorded as of the sale date partially offset by the adjustment to the investment banking fees discussed above.

In addition to the assumption of existing royalty obligations, King is required to pay Ligand a 15% royalty on AVINZA net sales during the first 20 months after Closing. Subsequent royalty payments will be based upon calendar year net sales. If calendar year net sales are less than $200.0 million, the royalty payment will be 5% of all net sales. If calendar year net sales are greater than $200.0 million, the royalty payment will be 10% of all net sales less than $250.0 million, plus 15% of net sales greater than $250.0 million. Royalty revenues were $20.3 million and $11.4 million in 2008 and 2007, respectively.

In connection with the sale, the Company has agreed to indemnify King for a period of 16 months after the closing of the Transaction for a number of specified matters, including any breach of the Company’s representations, warranties or covenants contained in the asset purchase agreement. In certain defined cases, the Company’s obligation to indemnify King extends for a period of 30 months following the closing of the Transaction. Under the Company’s agreement with King, $15.0 million of the total upfront cash payment was deposited into an escrow account to secure the Company’s indemnification obligations to King following the closing. Of the escrowed amount, $7.5 million was released to the Company on August 26, 2007, and the remaining $7.5 million, plus interest of $0.5 million, was released to the Company on February 26, 2008.

Under certain circumstances, the Company’s liability to King under the indemnification obligations of the asset purchase agreement may be in excess of the amounts deposited in the escrow account. The AVINZA asset purchase agreement also allows King, under certain circumstances, to offset indemnification claims against the royalty payments payable to the Company. Under the asset purchase agreement, the Company’s liability for any indemnification claim brought by King is generally limited to $40.0 million. However, the Company’s obligation to provide indemnification on certain matters is not subject to this indemnification limit. For example, the Company agreed to retain, and provide indemnification without limitation to King for all liabilities arising under

 

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certain agreements with Catalent related to the manufacture of AVINZA. The Company cannot predict the liabilities that may arise as a result of these matters. Any liability claims related to these matters or any indemnification claims made by King could materially and adversely affect the Company’s financial condition. No accrual for potential losses under the indemnification has been recorded at December 31, 2008 and 2007.

In connection with the Transaction, King loaned the Company $37.8 million (the “Loan”) which was used to pay the Company’s co-promote termination obligation to Organon due October 15, 2006. This loan was drawn, and the $37.8 million co-promote liability settled in October 2006. Amounts due under the loan were subject to certain market terms, including a 9.5% interest rate. In addition, and as a condition of the loan, $38.6 million of the funds received from Eisai was deposited into a restricted account to be used to repay the loan to King, plus interest. The Company repaid the loan plus interest in January 2007. As noted above, King refunded the interest to the Company on the Closing Date.

Also on September 6, 2006, the Company entered into a contract sales force agreement (the “Sales Call Agreement”) with King, pursuant to which King agreed to conduct a sales detailing program to promote the sale of AVINZA for an agreed upon fee, subject to the terms and conditions of the Sales Call Agreement. Pursuant to the Sales Call Agreement, King agreed to perform certain minimum monthly product details (i.e. sales calls), which commenced effective October 1, 2006 and continued until the Closing Date. Co-promotion expense recognized under the Sales Call Agreement for 2007 and 2006 was $2.8 million and $3.8 million, respectively. No amount was due to King under the Sales Call Agreement as of December 31, 2007. The Sales Call Agreement terminated effective on the Closing Date.

Assets and liabilities of the Company’s AVINZA product line on February 26, 2007 were as follows (in thousands):

 

ASSETS

  

Current assets:

  

Inventories, net (1)

   $ 2,926

Other current assets (2)

     2,780
      

Total current portion of assets disposed

     5,706
      

Equipment, net of accumulated depreciation (1)

     89

Acquired technology and product rights, net (1)

     82,174
      

Total long-term portion of assets disposed

     82,263
      

Total assets disposed

   $ 87,969
      

LIABILITIES

  

Current liabilities:

  

Deferred revenue, net (2)

   $ 49,324
      

Total liabilities disposed

   $ 49,324
      

 

(1) Represents assets acquired by King in accordance with the terms of the AVINZA Purchase Agreement.
(2) Represents assets or liabilities eliminated from the Company’s consolidated balance sheet in connection with the AVINZA sale transaction.

Prior to the AVINZA sale, the Company recorded accruals for rebates, chargebacks, and other discounts related to AVINZA products when product sales were recognized as revenue under the sell-through method. Upon the AVINZA sale, the Company accrued for rebates, chargebacks, and other discounts related to AVINZA products in the distribution channel which had not sold-through at the time of the AVINZA sale and for which the Company retained the liability subsequent to the sale. These products expire at various dates through June 30, 2009. The Company’s accruals for AVINZA rebates, chargebacks, and other discounts total $0.1 million and $1.0 million as of December 31, 2008 and 2007, respectively, and are included in accrued liabilities in the accompanying consolidated balance sheet.

 

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Additionally, and pursuant to the terms of the AVINZA Purchase Agreement, the Company retained the liability for returns of product from wholesalers that had been sold by the Company prior to the close of the transaction. Accordingly, as part of the accounting for the gain on the sale of AVINZA, the Company recorded a reserve for AVINZA product returns. AVINZA products sold by the Company may be returned through a specified period subsequent to the product expiration date, but no later than December 31, 2009. Under the sell-through revenue recognition method, the Company previously did not record a reserve for returns from wholesalers. The Company’s reserve for AVINZA returns is $8.2 million and $10.7 million as of December 31, 2008 and 2007, respectively, and is included in accrued liabilities in the accompanying consolidated balance sheet.

Results from Discontinued Operations

There was no activity related to discontinued operations for the year ended December 31, 2008.

The following table summarizes the 2007 results from discontinued operations included in the 2007 consolidated statement of operations (in thousands):

 

     AVINZA
Product
Line

Product sales

   $ 18,256
      

Operating costs and expenses:

  

Cost of products sold

     3,608

Research and development

     120

Selling, general and administrative

     3,709

Co-promotion

     2,814

Co-promote termination charges

     2,012
      

Total operating costs and expenses

     12,263
      

Income from operations

     5,993

Interest expense

     —  
      

Income before income taxes

   $ 5,993
      

The following table summarizes the 2006 results from discontinued operations included in the 2006 consolidated statement of operations (in thousands):

 

     Oncology
Product
Line
    AVINZA
Product
Line
    Total  

Product sales

   $ 47,512     $ 136,983     $ 184,495  

Collaborative research and development and other revenues

     208       —         208  
                        

Total revenues

     47,720       136,983       184,703  
                        

Operating costs and expenses:

      

Cost of products sold

     13,410       22,642       36,052  

Research and development

     12,895       380       13,275  

Selling, general and administrative

     13,891       36,118       50,009  

Co-promotion

     —         37,455       37,455  

Co-promote termination charges

     —         131,078       131,078  
                        

Total operating costs and expenses

     40,196       227,673       267,869  
                        

Income (loss) from operations

     7,524       (90,690 )     (83,166 )

Interest expense

     (51 )     (8,187 ) (1)     (8,238 )
                        

Income (loss) before income taxes

   $ 7,473     $ (98,877 )   $ (91,404 )
                        

 

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(1) As part of the terms of the AVINZA Purchase Agreement, the Company was required to redeem its outstanding convertible subordinated notes. All of the notes converted into shares of common stock in 2006 prior to redemption. In accordance with EITF 87-24, Allocation of Interest to Discontinued Operations , the interest on the notes was allocated to discontinued operations because the debt was required to be repaid in connection with the disposal transaction.

A comparison of sales by product for discontinued operations is as follows (in thousands):

 

     Years Ended December 31,
           2007                2006      

AVINZA

   $ 18,256    $ 136,983

ONTAK

     —        26,588

Targretin capsules

     —        17,575

Targretin gel and Panretin gel

     —        3,349
             

Total product sales

   $ 18,256    $ 184,495
             

5. Investments

As of December 31, 2008 and 2007, all of the Company’s investments have a contractual maturity of less than one year. The following table summarizes the various investment categories (in thousands):

 

     Cost    Gross
unrealized

gains
   Gross
unrealized

losses
    Estimated
fair
value

December 31, 2008

          

U.S. government securities

   $ 50,174    $ 81    $ —       $ 50,255

Corporate obligations

     1,663      —        —         1,663
                            
     51,837      81      —         51,918

Certificates of deposit—restricted

     1,341      —        —         1,341
                            

Total debt securities

   $ 53,178    $ 81    $ —       $ 53,259
                            

December 31, 2007

          

U.S. government securities

   $ 7,509    $ 4    $ —       $ 7,513

Corporate obligations

     10,078      14      (9 )     10,083
                            
     17,587      18      (9 )     17,596

Certificates of deposit—restricted

     1,411      —        —         1,411
                            

Total debt securities

   $ 18,998    $ 18    $ (9 )   $ 19,007
                            

On July 19, 2007, the Company purchased $5.0 million of commercial paper issued by Golden Key Ltd. While the investment was highly-rated and within the Company’s investment policy at the time of purchase, during the third quarter of 2007, large credit rating agencies downgraded the quality of this security. In addition, as a result of not meeting certain liquidity covenants, the assets were assigned to a trustee who established a committee of the largest senior credit holders to determine the next steps. Subsequently, Golden Key defaulted on its obligation to settle the security on the stated maturity date of October 10, 2007. Based on available information, management estimates that it will be able to recover approximately $1.7 million on this security. Accordingly, management adjusted the carrying value by recording an impairment loss of $2.0 million and $1.3 million in 2008 and 2007, respectively. This impairment is included in other income (expense) in the consolidated statement of operations. Further, liquidity in the capital markets has continued to be volatile. Accordingly, the Company may be exposed to additional impairment for this investment until it is fully recovered. There were no other material realized gains or losses on sales of available-for-sale securities for the years ended December 31, 2008, 2007, and 2006.

 

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6. Other Balance Sheet Details

Other current assets consist of the following (in thousands):

 

     December 31,
     2008    2007

Income taxes receivable

   $ 817    $ 3,099

Prepaid expenses

     1,147      1,076

Other receivables

     325      738

Other

     11      155
             
   $ 2,300    $ 5,068
             

Accrued liabilities consist of the following (in thousands):

 

     December 31,
     2008    2007

Warrant liability

   $ 670    $ —  

Compensation

     2,686      3,402

Legal

     4,166      —  

Restructuring costs

     848      —  

Other

     4,295      3,650
             
   $ 12,665    $ 7,052
             

The following summarizes the activity in the accounts related to allowances for loss on returns, rebates, chargebacks, and other discounts (in thousands):

 

     Charge-backs
and Rebates
    Returns     Total  

Balance at January 1, 2006

   $ 9,015     $ 6,714     $ 15,729  

Provision

     18,270       3,692       21,962  

Oncology Transaction Provision (1)

     2,276       10,020       12,296  

Payments

     (23,314 )     —         (23,314 )

Charges

     —         (11,985 )     (11,985 )
                        

Balance at December 31, 2006

     6,247       8,441       14,688  

Provision

     3,929       (1,243 ) (4)     2,686  

AVINZA Transaction Provision (2)

     1,953       19,355       21,308  

Oncology Transaction Provision (3)

     810       3,856       4,666  

Payments

     (10,723 )     —         (10,723 )

Charges

     —         (15,350 )     (15,350 )
                        

Balance at December 31, 2007

     2,216       15,059       17,275  

AVINZA Transaction Provision (2)

     (857 )     (211 )     (1,068 )

Oncology Transaction Provision (3)

     (49 )     (2,856 )     (2,905 )

Payments

     (802 )     —         (802 )

Charges

     —         (2,910 )     (2,910 )
                        

Balance at December 31, 2008

   $ 508     $ 9,082     $ 9,590  
                        

 

(1) The 2006 Oncology transaction provision amounts represent additional accruals recorded in connection with the sale of the Oncology Product Line to Eisai on October 25, 2006. The Company maintains the obligation for returns of product that were shipped to wholesalers prior to the close of the Eisai transaction on October 25, 2006 and chargebacks and rebates associated with product in the distribution channel as of the closing date.

 

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(2) The AVINZA transaction provision amounts represent additional accruals recorded in connection with the sale of the AVINZA Product Line to King Pharmaceuticals, Inc. on February 26, 2007. The Company maintains the obligation for returns of product that were shipped to wholesalers prior to the close of the King transaction on February 26, 2007 and chargebacks and rebates associated with product in the distribution channel as of the closing date.
(3) The 2007 Oncology transaction provision amounts represent changes in the estimates of the accruals for chargebacks and rebates recorded in connection with the sale of the Oncology Product Line.
(4) The credit for returns in 2007 primarily consists of a change in the estimate of ONTAK end-customer returns. The accrual for ONTAK end-customer returns is a result of the operations of the Oncology Product Line prior to its sale on October 25, 2006.

7. AVINZA Co-Promotion

In February 2003, Ligand and Organon Pharmaceuticals USA Inc. (Organon) announced that they had entered into an agreement for the co-promotion of AVINZA. Subsequently in January 2006, Ligand signed an agreement with Organon that terminated the AVINZA co-promotion agreement between the two companies and returned AVINZA co-promotion rights to Ligand. The termination was effective as of January 1, 2006; however, the parties agreed to continue to cooperate during a transition period that ended September 30, 2006 (the “Transition Period”) to promote the product. The Transition Period co-operation included a minimum number of product sales calls per quarter as well as the transition of ongoing promotions, managed care contracts, clinical trials and key opinion leader relationships to Ligand. During the Transition Period, Ligand paid Organon an amount equal to 23% of AVINZA net sales. Ligand also paid and was responsible for the design and execution of all clinical, advertising and promotion expenses and activities.

Additionally, in consideration of the early termination and return of rights under the terms of the agreement, Ligand agreed to and paid Organon $37.8 million in October 2006. Ligand further agreed to and paid Organon $10.0 million in January 2007, in consideration of the minimum sales calls during the Transition Period. In addition, following the Transition Period, Ligand agreed to make quarterly royalty payments to Organon equal to 6.5% of AVINZA net sales through December 31, 2012 and thereafter 6.0% through patent expiration, currently anticipated to be November of 2017.

The unconditional payment of $37.8 million to Organon and the estimated fair value of the amounts to be paid to Organon after the termination ($95.2 million as of January 1, 2006), based on the estimated net sales of the product (currently anticipated to be paid quarterly through November 2017), were recognized as liabilities and expensed as costs of the termination as of the effective date of the agreement, January 1, 2006. Additionally, the conditional payment of $10.0 million, which represents an approximation of the fair value of the service element of the agreement during the Transition Period (when the provision to pay 23% of AVINZA net sales is also considered), was recognized ratably as additional co-promotion expense over the Transition Period.

As more fully described in Note 4, on February 26, 2007, Ligand and King executed an agreement pursuant to which King acquired all of the Company’s rights in and to AVINZA, assumed certain liabilities, and reimbursed Ligand the $47.8 million previously paid to Organon (comprised of the $37.8 million paid in October 2006 and the $10.0 million that the Company paid in January 2007). King also assumed the Company’s co-promote termination obligation to make royalty payments to Organon based on net sales of AVINZA. For the fourth quarter of 2006 and through the closing of the AVINZA sale transaction, amounts owed by Ligand to Organon on net reported sales of AVINZA did not result in current period expense, but instead were charged against the co-promote termination liability. The liability was adjusted at each reporting period to fair value and was recognized, utilizing the interest method, as additional co-promote termination charges for that period at a rate of 15%, the discount rate used to initially value this component of the termination liability.

In connection with King’s assumption of this obligation, Organon did not consent to the legal assignment of the co-promote termination obligation to King. Accordingly, Ligand remains liable to Organon in the event of

 

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King’s default of the obligation. Therefore, Ligand recorded an asset as of February 26, 2007 to recognize King’s assumption of the obligation, while continuing to carry the co-promote termination liability in the Company’s consolidated financial statements to recognize Ligand’s legal obligation as primary obligor to Organon as required under SFAS No. 140, Accounting for Transfers and Servicing of Financial Assets and Extinguishments of Liabilities . This asset represents a non-interest bearing receivable for future payments to be made by King and is recorded at its fair value. As of December 31, 2007 and thereafter, the receivable and liability will remain equal and adjusted each quarter for changes in the fair value of the obligation including for any changes in the estimate of future net AVINZA product sales. This receivable will be assessed on a quarterly basis for impairment (e.g. in the event King defaults on the assumed obligation to pay Organon). As of December 31, 2007, the fair value of the co-promote termination liability (and the corresponding receivable) was reduced by $36.7 million based on revised estimated future net AVINZA product sales using a discount rate of 15%.

On an annual basis, management reviews the carrying value of the co-promote termination liability. Due to assumptions and judgments inherent in determining the estimates of future net AVINZA sales through November 2017, the actual amount of net AVINZA sales used to determine the current fair value of the Company’s co-promote termination asset and liability may be materially different from current estimates.

A summary of the co-promote termination liability as of December 31, 2008 and 2007 is as follows (in thousands):

 

Net present value of payments based on estimated future net AVINZA product sales as of December 31, 2006

   $ 93,328  

Payment made in February 2007 to Organon for net AVINZA sales from October 1, 2006 through December 31, 2006

     (2,218 )

Payment made in May 2007 to Organon for net AVINZA sales from January 1, 2007 through February 26, 2007

     (1,187 )

Assumed payments made by King or assignee in 2007

     (4,943 )

2007 fair value adjustments due to passage of time

     11,183  

December 31, 2007 adjustment based on revised estimated future payments based on revised estimated future net AVINZA product sales

     (36,707 )
        

Net present value of payments based on estimated future net AVINZA product sales as of December 31, 2007

   $ 59,456  

Assumed payments made by King or assignee

     (8,803 )

Fair value adjustments due to passage of time

     7,829  
        

Total co-promote termination liability as of December 31, 2008

     58,482  

Less: remaining current portion of co-promote termination liability as of December 31, 2008

     (10,958 )
        

Long-term portion of co-promote termination liability as of December 31, 2008

   $ 47,524  
        

8. Note Payable

In December 2006, Pharmacopeia entered into a loan and security agreement (the Line of Credit) with a lending institution to provide up to a total of $5.0 million in funding in the form of term loans, from time to time through December 2008. Term loans secured by laboratory equipment have a fixed term of 48 months. Term loans secured by all other collateral categories have a fixed term of 36 months.

As of December 31, 2008, the aggregate balance of term loans originated under the Line of Credit was approximately $3.4 million, of which approximately $2.1 million was classified as equipment financing obligations, long-term. Interest rates on these term loans range from 10.08% to 10.28%. The Company paid off the Line of Credit in full in January 2009.

 

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9. Warrant Liability

In connection with the acquisition of Pharmacopeia, the Company assumed approximately 867,637 warrants (as adjusted as a result of the merger from the original 1,450,000) to purchase its common stock. Under EITF 00-19, to qualify as permanent equity, an equity derivative must permit the issuer to settle in unregistered shares. Under securities law, if the warrants were issued in connection with a public offering and have a cash settlement feature at the holder’s option, a company does not have the ability to settle in unregistered shares. Therefore, the warrants cannot be classified as permanent equity and are instead classified as a liability. The warrants issued as part of Pharmacopeia’s equity financing in October 2006 meet this criteria, and have been recorded as a liability in the accompanying balance sheet. The fair value of the warrants will be remeasured at each reporting date until the warrants are exercised or have expired. Changes in the fair value of the warrants are reported in the statement of operations as income (decreases) or expense (increases).

At December 31, 2008, the fair value of the warrants was approximately $0.7 million and included in accrued liabilities.

The fair value of the warrants was calculated using the Black-Scholes option-pricing model with the following assumptions at December 31, 2008:

 

Risk-free interest rate

   1.0%

Dividend yield

   —  

Expected volatility

   78%

Expected term

   3.3 years

10. Commitments and Contingencies

ECLiPS ® Royalties

Under its license agreement with the Trustees of Columbia (Columbia) University and Cold Spring Harbor Laboratory (Cold Spring) (the “License Agreement”), the Company has an exclusive license for technology used in its proprietary combinatorial chemistry encoding technology, Encoded Combinatorial Libraries on Polymeric Support, or ECLiPS ® . The License Agreement obligates the Company to pay a minimum annual license fee of $0.1 million to both Columbia and Cold Spring. The License Agreement expires upon the later of (i) July 16, 2013 or (ii) the expiration of the last patent relating to the technology, at which time the Company will have a fully paid license to the technology. The license granted to the Company under the License Agreement can be terminated by Columbia and Cold Spring (i) upon 30 days written notice to the Company if the Company materially breaches the Agreement and the Company fails to cure such material breach in accordance with the License Agreement or (ii) if the Company commits any act of bankruptcy, becomes insolvent, files a petition under any bankruptcy or insolvency act or has any such petition filed against it that is not dismissed within 60 days. The Company is also obligated to pay royalties to Columbia and Cold Spring based on net sales of pharmaceutical products the Company develops, as well as a percentage of all other revenue the Company recognizes from collaborators that is derived from the technology licensed from Columbia and Cold Spring.

Property Leases

The Company leases an 82,500 square foot office and laboratory facility in San Diego, California through November 2021. Under the terms of the lease, the Company pays a basic annual rent of $3.0 million (subject to an annual fixed percentage increase, as set forth in the agreement), plus a 1% annual management fee, property taxes and other normal and necessary expenses associated with the lease including but not limited to utilities and repairs and maintenance. The Company has the right to extend the lease for two five-year terms and will have the first right of refusal to lease, at market rates, any facilities built on the sold lots.

 

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The Company also leases an office and research facility in San Diego, California under an operating lease arrangement through July 2015. The Company fully vacated this facility in February 2008. The lease agreement provides for increases in annual rents based on changes in the Consumer Price Index or fixed percentage increases ranging from 3% to 7%. Commencing January 2008, the Company sublet this facility through July 2015. The sublease agreement provides for a 3% increase in annual rents. As of December 31, 2008, the Company expects to receive aggregate future minimum lease payments totaling $5.7 million (nondiscounted) over the duration of the sublease agreement. In accordance with SFAS No. 146 (As Amended) “Accounting for Costs Associated with Exit or Disposal Activities,” the Company recorded a net charge to operating expenses of $4.3 million for exit costs when it fully ceased use of this facility in the first quarter of 2008. The net charge consisted of a $6.5 million charge for future rent payments offset by a $2.3 million reversal of deferred rent. As of December 31, 2008, annual minimum rentals expected to be received by the Company under the sublease are as follows (in thousands):

 

Year ending December 31,

    

2009

   $ 812

2010

     829

2011

     854

2012

     879

2013

     906

Thereafter

     1,412
      
   $ 5,692
      

The Company leases approximately 99,000 square feet in three facilities in Cranbury, New Jersey under leases that expire in 2016. The leases for the New Jersey facilities provide generally for scheduled rent increases, options to extend the leases with certain changes to the terms of the lease agreement, and refurbishment allowances.

Total rent expense under all office leases for 2008, 2007 and 2006 was $11.0 million, $5.4 million, and $2.4 million, respectively. The Company recognizes rent expense on a straight-line basis. Deferred rent at December 31, 2008 and 2007 was $1.4 million and $3.1 million, respectively, and is included in other long-term liabilities.

Equipment Financing

The Company has entered into capital lease and equipment agreements that require monthly payments through September 2010 including interest ranging from 8.36% to 10.11%. The cost of equipment under these agreements at December 31, 2008 and 2007 was $5.5 million and $5.8 million, respectively. At December 31, 2008 and 2007, related accumulated amortization was $4.6 million and $3.9 million, respectively. The underlying equipment is used as collateral under the equipment financing.

In addition, as of December 31, 2008, Pharmacopeia had a $3.4 million Line of Credit balance in the form of term loans secured by laboratory and other underlying collateral. The line of credit was paid in full as of January 2009.

 

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At December 31, 2008 annual minimum payments due under the Company’s office and equipment lease obligations, excluding any sublease income, and equipment financing obligations are as follows (in thousands):

 

     Equipment
financing
obligations
    Operating
leases

2009

   $ 2,141     $ 7,815

2010

     1,583       7,968

2011

     766       8,126

2012

     16       8,288

2013

     —         8,455

Thereafter

     —         42,502
              

Total minimum lease payments

     4,506     $ 83,154
        

Less: amounts representing interest

     (4,994 )  
          

Present value of minimum lease payments

     4,007    

Less: current portion

     (1,829 )  
          
   $ 2,178    
          

Product Liability

The Company’s business exposes it to potential product liability risks. The Company’s products also may need to be recalled to address regulatory issues. A successful product liability claim or series of claims brought against the Company could result in payment of significant amounts of money and divert management’s attention from running the business. Some of the compounds the Company is investigating may be harmful to humans. For example, retinoids as a class are known to contain compounds which can cause birth defects. The Company may not be able to maintain insurance on acceptable terms, or the insurance may not provide adequate protection in the case of a product liability claim. To the extent that product liability insurance, if available, does not cover potential claims, the Company would be required to self-insure the risks associated with such claims.

Litigation

SEC Investigation

The SEC issued a formal order of private investigation dated September 7, 2005, to investigate the circumstances surrounding restatement of our consolidated financial statements for the years ended December 31, 2002 and 2003, and for the first three quarters of 2004. The SEC’s investigation is ongoing and the Company is cooperating with the investigation.

Other Matters

The Company and Seragen, Inc., a subsidiary, were named parties to Sergio M. Oliver, et al. v. Boston University, et al. , a shareholder class action filed on December 17, 1998 in the Court of Chancery in the State of Delaware. The Company and Seragen were dismissed from the action, but such dismissal is subject to appeal and the Company and Seragen may have possible indemnification obligations with respect to certain defendants. As of December 31, 2008, the Company had not accrued an indemnification obligation based on management’s assessment that its responsibility for any such obligation is not probable or estimable.

In July 2007, the Salk Institute for Biological Studies (Salk) filed a demand for arbitration with the American Arbitration Association, seeking damages for alleged breach of contract based on Salk’s theory that it is entitled to a portion of the money paid by Eisai to the Company for Targretin related assets. In September 2008, the Company reached a settlement with Salk, whereby the parties resolved all disputes that had arisen

 

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between them, including Salk’s primary claim in arbitration relating to the sale of Targretin to Eisai in 2006. As part of the settlement, the parties executed mutual releases and agreed to jointly seek dismissal with prejudice of all claims and counterclaims asserted in the arbitration. The Company agreed to pay Salk a total of $13.0 million, which was recorded as research and development expense in 2008, of which $9.5 million was due immediately upon settlement and $3.5 million due six months from the date of settlement in return for which Salk acknowledged that no additional payments would be due from Ligand or any sublicensee for any past, present or future conduct, including development of any compound in Ligand’s internal or partnered pipeline, except for any future bazedoxifene related payments. Pursuant to the parties’ agreement, the American Arbitration Association dismissed the proceeding. As of December 31, 2008, the Company had recorded a liability of $3.5 million related to the settlement, which is included in current portion of accrued litigation settlement costs in the accompanying balance sheets.

On March 4, 2008, The Rockefeller University (Rockefeller) filed suit, now proceeding in the United States District Court for the Southern District of New York, against the Company alleging, among other things, a breach by the Company of their September 30, 1992 license agreement with Rockefeller, as well as other causes of action for unjust enrichment, quantum meruit, specific performance to perform an audit and declaratory relief. In February 2009, the Company reached a settlement with Rockefeller whereby the parties resolved all disputes that have arisen between them, including Rockefeller’s primary claim relating to the development of PROMACTA as well the Company’s counterclaims. As part of the settlement, the parties executed mutual releases and agreed to jointly seek dismissal with prejudice of all claims, demands and causes of action, whether known or unknown, arising out of or based upon the license agreement, the ongoing litigation, PROMACTA, LGD-4665, and any other compound developed by the Company that was subject to the license agreement. The Company also agreed to pay Rockefeller, $5.0 million immediately upon settlement, $1.0 million on or before February 10, 2010, $1.0 million on or before February 10, 2011, and 50% of any milestone payment and 5.88% to 7.0% of certain royalties, in each case received by the Company pursuant to an agreement with SmithKline Beecham Corporation (now known as GlaxoSmithKline) entered into on December 29, 1994. The Company also agreed to pay Rockefeller 1.5% of world-wide net sales of LGD-4665 as certain payments are received by the Company pursuant to its agreement with SmithKline Beecham Corporation entered into on December 17, 2008. As of December 31, 2008, the Company has recorded a liability of $7.0 million related to the settlement, of which $5.0 million is included in current portion of accrued litigation settlement costs and $2.0 million is included in other long term liabilities in the accompanying balance sheets.

On October 10, 2008, the Company received notice that a putative class action complaint was filed in the Superior Court of New Jersey, Mercer County (Equity Division) by Allen Heilman, one of Phamacopeia’s stockholders, against Pharmacopeia, the members of its Board of Directors, the Company and two of our wholly owned subsidiaries. The complaint generally alleges that Pharmacopeia’s Board of Directors’ decision to enter into the proposed transaction with the Company on the terms contained in the proposed merger agreement constitutes a breach of fiduciary duty and gives rise to other unspecified state law claims. The complaint also alleges that the Company and two of our wholly owned subsidiaries aided and abetted Pharmacopeia’s Board of Directors’ breach of fiduciary duty. In addition, the complaint alleges that the named plaintiff will seek “equitable relief,” including among other things, an order preliminarily and permanently enjoining the proposed transaction. While the Company believes that neither Ligand nor Pharmacopeia engaged in any wrongful acts, in an effort to minimize the cost and expense of any litigation, in December 2008, the Company entered into a memorandum of understanding, or MOU, with the named plaintiff providing for the settlement of the lawsuit. Subject to court approval and further definitive documentation, the MOU provides a release and settlement by the purported class of all claims against Pharmacopeia, the Company, and the Company’s affiliates and agents in connection with the complaint. Pursuant to the MOU the Company has agreed not to oppose any fee application by plaintiffs’ counsel that does not exceed $180,000. As of December 31, 2008, the Company has recorded a liability of $0.2 million related to the MOU.

In addition, from time to time the Company is subject to various lawsuits and claims with respect to matters arising out of the normal course of the Company’s business. Due to the uncertainty of the ultimate outcome of these matters, the impact on future financial results is not subject to reasonable estimates.

 

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Funding of Legacy Director Indemnity Fund

On March 1, 2007, the Company entered into an indemnity fund agreement, which established in a trust account with Dorsey & Whitney LLP, (Dorsey) counsel to the Company’s independent directors and to the Audit Committee of the Company’s Board of Directors, a $10.0 million indemnity fund to support the Company’s existing indemnification obligations to continuing and departing directors in connection with the ongoing SEC investigation and related matters. Ligand has agreed to supplement the indemnity fund upon Dorsey’s request should the fund become insufficient to cover liabilities and defense costs required to be paid under the Company’s indemnification agreements. Upon the earlier of (i) the resolution of the SEC investigation and related matters, (ii) the expiration of 24 months after receipt of any written or oral communication initiated by the SEC regarding the investigation, (iii) written communications from the SEC that the investigation has been discontinued, or (iv) otherwise by the mutual agreement of the parties to terminate the indemnity fund agreement, Dorsey will remit the remaining balance of the fund to Ligand. The balance of this fund, amounting to $10.2 million and $10.1 million, has been recorded as restricted indemnity account in the consolidated balance sheets as of December 31, 2008 and 2007, respectively.

11. Common Stock Subject to Conditional Redemption—Pfizer Settlement Agreement

In April 1996, the Company and Pfizer entered into a settlement agreement with respect to a lawsuit filed in December 1994 by the Company against Pfizer. In connection with a collaborative research agreement the Company entered into with Pfizer in 1991, Pfizer purchased shares of the Company’s common stock. Under the terms of the settlement agreement, at the option of either the Company or Pfizer, milestone and royalty payments owed to the Company can be satisfied by Pfizer by transferring to the Company shares of the Company’s common stock at the exchange ratio of $12.375 per share. In accordance with EITF D-98, the remaining common stock issued and outstanding to Pfizer following the settlement was reclassified as common stock subject to conditional redemption (between liabilities and equity) since Pfizer has the option to settle milestone and royalties payments owed to the Company with the Company’s shares, and such option is not within the Company’s control. At December 31, 2008 and 2007, respectively, the remaining shares of the Company’s common stock that could be redeemed totaled approximately 998,000, which are reflected at the exchange ratio price of $12.375 for a total of $12.3 million. As of December 31, 2008, no cash payments or transfers of shares have been made.

12. Stockholders’ Equity

Stock Plans

The 2002 Stock Incentive Plan contains five separate equity programs – Discretionary Option Grant Program, Automatic Option Grant Program, Stock Issuance Program, Director Fee Option Grant Program and Other Stock Award Program (the “2002 Plan”). On May 31, 2007, shareholders of the Company approved an amendment and restatement of the 2002 Plan. As of December 31, 2008, 2,142,800 shares remained available for future option grant or direct issuance.

The Company grants options to employees, non-employee consultants, and non-employee directors. Non-employee directors are accounted for as employees under SFAS 123R. Options and restricted stock granted to certain directors vest in equal monthly installments over one year from the date of grant. Options granted to employees vest 1/8 on the six month anniversary of the date of grant, and 1/48 each month thereafter for forty-two months. All option awards generally expire ten years from the date of grant.

Stock-based compensation cost for awards to employees and non-employee directors is recognized on a straight-line basis over the vesting period until the last tranche vests. Compensation cost for consultant awards is recognized over each separate tranche’s vesting period. The Company recognized compensation expense of $3.6 million, $7.6 million and $5.3 million for 2008, 2007 and 2006, respectively, associated with option awards, restricted stock and an equitable adjustment of employee stock options. Of the total compensation expense

 

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associated with option awards, $0.3 million related to options granted to non-employee consultants for 2006. Of the total compensation expense associated with the option awards for 2007, $1.8 million related to the $2.50 equitable adjustment of the exercise price for all options outstanding as of April 3, 2007 that was measured for financial reporting purposes effective March 28, 2007, the date the Compensation Committee of the Company’s Board of Directors approved the adjustment. There was no deferred tax benefit recognized in connection with these costs.

The fair-value for options that were awarded to employees and directors was estimated at the date of grant using the Black-Scholes option valuation model with the following weighted average assumptions:

 

     Years Ended December 31,  
     2008     2007     2006  

Risk-free interest rate

   3.0 %   4.9 %   4.8 %

Dividend yield

   —       —       —    

Expected volatility

   65 %   66 %   70 %

Expected term

   6 years     6 years     6 years  

The expected term of the employee and non-employee director options is the estimated weighted-average period until exercise or cancellation of vested options (forfeited unvested options are not considered). SAB 107 guidance permits companies to use a “safe harbor” expected term assumption for grants up to December 31, 2007 based on the mid-point of the period between vesting date and contractual term, averaged on a tranche-by-tranche basis. The Company used the safe harbor in selecting the expected term assumption in 2007. The expected term for consultant awards is the remaining period to contractual expiration.

Volatility is a measure of the expected amount of variability in the stock price over the expected life of an option expressed as a standard deviation. SFAS 123(R) requires an estimate of future volatility. In selecting this assumption, the Company used the historical volatility of the Company’s stock price over a period equal to the expected term.

 

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Following is a summary of the Company’s stock option plan activity and related information:

 

     Shares     Weighted
Average
Exercise
Price
    Weighted-
Average
Remaining
Contractual
Term in
Years
   Aggregate
Intrinsic
Value

(In thousands)

Balance at January 1, 2006

   7,001,657     $ 11.76       

Granted

   1,268,696       10.88       

Exercised

   (1,227,830 )     8.66       

Forfeited

   (404,654 )     9.89       

Cancelled

   (871,483 )     13.00       
             

Balance at December 31, 2006

   5,766,386       10.43 (A)   6.04    $ 4,602

Granted

   843,936       7.06       

Exercised

   (648,277 )     6.87       

Forfeited

   (589,893 )     8.25       

Cancelled

   (3,149,120 )     11.71       
             

Balance at December 31, 2007

   2,223,032       8.87     5.17      304

Granted

   1,304,500       3.52       

Exercised

   (4,438 )     3.41       

Forfeited

   (107,058 )     6.88       

Cancelled

   (385,960 )     9.64       
             

Balance at December 31, 2008

   3,030,076       6.55     6.63      81
             

Exercisable at December 31, 2008

   1,579,233       8.44     4.86      81

Options expected to vest as of December 31, 2008

   2,854,346       6.69     6.51      81

 

(A) Adjusted to reflect April 2007 equitable adjustment

The weighted-average grant-date fair value of all stock options granted during 2008 was $2.15 per share. The total intrinsic value of all options exercised during 2008 and 2007 was approximately $3,000 and $1.7 million, respectively. As of December 31, 2008, there was $3.4 million of total unrecognized compensation cost related to nonvested stock options. That cost is expected to be recognized over a weighted average period of 2.7 years.

Cash received from options exercised in 2008 and 2007 was $15,000 and $4.2 million, respectively. As of December 31, 2007, there were approximately $0.2 million of receivables related to stock option exercises which were subsequently received in January 2008. There is no current tax benefit related to options exercised because of Net Operating Losses (NOLs) for which a full valuation allowance has been established.

Following is a further breakdown of the options outstanding as of December 31, 2008:

 

     Options Outstanding    Options exercisable

Range of exercise prices

   Options
outstanding
   Weighted
average
remaining life
in years
   Weighted
average

exercise price
   Options
exercisable
   Weighted
average

exercise price

$0.01–$3.45

   108,766    4.61    $ 2.164    98,142    $ 2.03

  3.46–  3.50

   1,242,500    8.87      3.50    238,017      3.50

  3.51–  7.15

   659,625    7.75      6.60    273,372      6.63

  7.16–10.52

   615,287    3.76      8.93    565,804      8.94

10.75–14.66

   403,898    2.87      13.42    403,898      13.42
                  

  0.01–14.66

   3,030,076    6.63    $ 6.55    1,579,233    $ 8.44
                  

 

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Restricted Stock Activity

The following is a summary of the Company’s restricted stock activity and related information:

 

     Shares     Weighted-Average
Grant Date

Fair Value

Nonvested at December 31, 2006

   1,297     $ 11.56

Granted

   320,300       9.69

Vested

   (1,297 )     11.56

Forfeited

   (24,700 )     7.15
        

Nonvested at December 31, 2007

   295,600       9.90

Granted

   434,000       3.38

Vested

   (110,012 )     10.92

Forfeited

   (20,916 )     5.43
        

Nonvested at December 31, 2008

   598,672       5.14
        

Restricted stock awards generally vest over three years. As of December 31, 2008, unrecognized compensation cost related to non-vested stock awards amounted to $1.0 million. That cost is expected to be recognized over a weighted average period of 1.6 years.

Preferred Stock

The Company has authorized 5,000,000 shares of preferred stock, of which 1,600,000 are designated Series A Participating Preferred Stock (the “Preferred Stock”). The Board of Directors of Ligand has the authority to issue the Preferred Stock in one or more series and to fix the designation, powers, preferences, rights, qualifications, limitations and restrictions of the shares of each such series, including the dividend rights, dividend rate, conversion rights, voting rights, rights and terms of redemption (including sinking fund provisions), liquidation preferences and the number of shares constituting any such series, without any further vote or action by the stockholders. The rights and preferences of Preferred Stock may in all respects be superior and prior to the rights of the common stock. The issuance of the Preferred Stock could decrease the amount of earnings and assets available for distribution to holders of common stock or adversely affect the rights and powers, including voting rights, of the holders of the common stock and could have the effect of delaying, deferring or preventing a change in control of Ligand. As of December 31, 2008 and 2007, there are no preferred shares issued or outstanding.

Shareholder Rights Plan

In October 2006, the Company’s Board of Directors renewed the Company’s stockholder rights plan, which was originally adopted and has been in place since September 2002, and which expired on September 13, 2006, through the adoption of a new 2006 Stockholder Rights Plan (the “2006 Rights Plan”). The 2006 Rights Plan provides for a dividend distribution of one preferred share purchase right (a “Right”) on each outstanding share of the Company’s common stock. Each Right entitles stockholders to buy 1/1000th of a share of Ligand Series A Participating Preferred Stock at an exercise price of $100. The Rights will become exercisable if a person or group announces an acquisition of 20% or more of the Company’s common stock, or announces commencement of a tender offer for 20% or more of the common stock. In that event, the Rights permit stockholders, other than the acquiring person, to purchase the Company’s common stock having a market value of twice the exercise price of the Rights, in lieu of the Preferred stock. In addition, in the event of certain business combinations, the Rights permit the purchase of the common stock of an acquiring person at a 50% discount. Rights held by the acquiring person become null and void in each case. The 2006 Rights Plan expires in 2016.

 

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Cash Dividend

On March 22, 2007, the Company declared a cash dividend on the common stock of the Company of $2.50 per share. As the Company has an accumulated deficit, the dividend was recorded as a charge against additional paid-in capital in the first quarter of 2007. The aggregate amount of $252.7 million was paid on April 19, 2007 to shareholders of record as of April 5, 2007.

Modification to Employee Stock Options

In February 2007, the Company’s shareholders approved a modification to the 2002 Stock Incentive Plan (the “2002 Plan”) to allow equitable adjustments to be made to options outstanding under the 2002 Plan. Effective April 2007, the Company reduced the exercise price by $2.50 (or to the par value of the stock for those options with an exercise price below $2.50 per share), as an equitable adjustment, for all options then outstanding under the 2002 Plan to reflect the special cash dividend. Under the requirements of SFAS 123(R), the Company recognized $1.8 million of stock compensation expense in connection with the equitable adjustment effective March 28, 2007, the date the Compensation Committee of the Company’s Board of Directors approved the equitable adjustment.

Shares Issued in Business Combination

On December 23, 2008, in connection with its acquisition of Pharmacopeia, the Company issued 17,997,039 shares of common stock to Pharmacopeia stockholders, or 0.5985 shares for each outstanding Pharmacopeia share.

Warrants

As of December 31, 2008, warrants to purchase 867,637 shares of the Company’s common stock were outstanding with an exercise price of $8.59 per share and warrants to purchase 105,554 shares of the Company’s common stock were outstanding with an exercise price of $9.47 per share. The warrants were assumed in connection with the acquisition of Pharmacopeia, Inc. and expire in April 2012 and March 2011, respectively.

Share Repurchases

In March 2007, the Board of Directors authorized up to $100.0 million in share repurchases over the subsequent 12 months. In 2007, the Company repurchased 6.2 million shares of its common stock totaling $39.6 million. Subsequent to December 31, 2007 and through February 28, 2008, the Company repurchased an additional 0.3 million shares of its common stock totaling $1.6 million.

13. Collaboration Agreements and Royalty Matters

AVINZA Royalty

In connection with the sale of the Company’s AVINZA product line to King, King is required to pay Ligand a 15% royalty on AVINZA net sales during the first 20 months after the Closing Date, February 26, 2007. Subsequent royalty payments will be based upon calendar year net sales. If calendar year net sales are less than $200.0 million, the royalty payment will be 5% of all net sales. If calendar year net sales are greater than $200.0 million, the royalty payment will be 10% of all net sales less than $250.0 million, plus 15% of net sales greater than $250.0 million.

Collaborative Research and Development Programs

The Company has entered into multiple research and development collaboration arrangements with third party pharmaceutical companies. The commercial terms of such arrangements typically include some combination of the following types of fees: exclusivity fees, technology access fees, technology development fees and research support payments, as well as milestone payments, license or commercialization fees. The

 

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Company may also receive royalties on product candidates resulting from its research and development collaboration arrangements if and to the extent any such product candidate is ultimately approved by the FDA and successfully marketed. The Company’s collaborations are discussed below.

Bristol-Myers Squibb Collaborations

DARA Program

In connection with the completion of the Company’s acquisition of Pharmacopeia, the Company assumed an exclusive licensing agreement with BMS, originally entered into in March 2006, which provides the Company with an exclusive license under certain BMS patents with respect to worldwide development and commercialization of PS433540, as well as certain other compounds discovered by BMS that possess DARA activity.

Under the terms of the DARA license agreement, in lieu of an up-front cash payment, the Company is providing BMS a set of compound libraries, over a period of approximately three years following the execution of the DARA license agreement. In the event the Company fails to deliver such compound libraries to BMS, the Company would be required to make cash payments to BMS on a pro rata basis of up to $0.1 million as of December 31, 2008.

Under the terms of the DARA license agreement, the Company is obligated to pay BMS milestone payments upon the achievement, if any, of further successive clinical and regulatory events in the United States and certain other jurisdictions, and a stepped royalty based on net sales of products, if any, resulting from the DARA program. BMS has a limited right of first negotiation in the event that the Company desires to license compounds that are the subject of the DARA license agreement to a third party other than BMS.

SARM Program

In connection with the Company’s acquisition of Pharmacopeia, the Company assumed an exclusive licensing agreement with BMS, originally entered into in October 2007, which provides the Company exclusive worldwide development and commercialization rights to a SARM program, including PS178990, for which a Phase I single ascending dose study had been completed. PS178990 is a non-steroidal SARM that was designed to provide the benefits of testosterone to patients without unwanted side effects on the prostate.

Under the SARM license agreement, the Company is required to make milestone payments to BMS upon the submission and approval of a therapeutic product for marketing in the United States and certain other jurisdictions and is obligated to make milestone payments to BMS upon achieving certain worldwide annual net sales of products resulting from the SARM program. The Company is also obligated to pay to BMS a stepped royalty on annual net sales on products covered by the SARM License agreement. BMS has a limited right of first negotiation in the event that the Company attempts to license compounds that are the subject of the SARM License agreement to a third party other than BMS.

The Company also assumed a discovery collaboration agreement with BMS to provide a portion of its medicinal chemistry resources to a BMS discovery program unrelated to the SARM program for a period up to three years beginning in October 2007. The discovery collaboration agreement provides that each such year, the Company is required to provide a fixed number of full-time workers for the BMS discovery program, divided between employees located at its facility in Cranbury, New Jersey and contracted headcount located outside the United States.

In addition, the Company agreed to pay milestone payments to BMS associated with the submission and approval of a therapeutic product for marketing and a stepped royalty on net sales of therapeutic products, if any, resulting from the SARM program. BMS has a limited right of first negotiation in the event that the Company desires to license compounds that are the subject of the SARM License agreement to a third party other than BMS.

As of December 31, 2008, the Company had deferred revenue of approximately $13.0 million related to BMS agreements.

 

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GlaxoSmithKline Collaboration

Agreement with Pharmacopeia

In connection with the completion of the Company’s acquisition of Pharmacopeia, the Company assumed a product development and commercialization agreement which Pharmacopeia and SmithKlineBeecham Corporation and Glaxo Group Limited (together GSK) entered into in March 2006. The Company’s role in the collaboration is to identify and advance molecules in chosen therapeutic programs to development stage and, subject to certain provisions in the GSK agreement, further develop the candidates to clinical “proof of concept” (a demonstration of efficacy in humans). The Company agreed that it will not screen its compound library for other collaborators, or for its own account, against any target it screens under the GSK agreement for a specified period.

The GSK agreement provides GSK an exclusive option, exercisable at defined points during the development process for each program up to “proof of concept,” to license that program. Upon licensing a program, GSK is obligated to conduct preclinical development and/or clinical trials and commercialize pharmaceutical products, if any, resulting from such licensed programs on a worldwide basis. The Company is entitled to receive success-based milestone payments, starting in preclinical research, from GSK for each drug development program under the alliance and the potential for double-digit royalties upon the successful commercialization by GSK of any product resulting therefrom.

In the event that GSK does not exercise its option to license a program, the Company will retain all rights to that program and may continue to develop the program and commercialize any products resulting from the program, or the Company may elect to cease progressing the program and/or seek other partners for further development and commercialization. Should the Company develop or partner such a program and commercialize any products resulting from that program, it will be obligated to pay GSK success-based milestone payments and royalties upon successful commercialization, if any.

Pharmacopeia received $15.0 million in connection with initial discovery activities which the Company is obligated to perform under the GSK agreement. The Company recognizes revenue on a percentage of completion basis as it performs the required discovery activities in an amount from time to time less than or equal to the non-refundable portion of payments received in connection with the GSK agreement. The initial research term of the GSK agreement expires in March 2011. As of December 31, 2008, the Company had deferred revenue of approximately $6.3 million related to GSK agreements.

The Company and GSK each have the right to terminate the GSK agreement in their sole discretion under certain specified circumstances at any time during the term of the GSK agreement. In addition, the Company and GSK each have the right to terminate the GSK agreement under other circumstances that are customary in these types of agreements. If the Company exercises its discretionary termination right at any time during the first five years of the term, under certain circumstances, the Company could be required to refund to GSK a portion of the $15.0 million referred to above which it received related to its initial discovery activities. The amount of any such refund will be calculated based upon when during the term of the GSK agreement that termination occurs and the amount of research funding the Company had received prior to such termination. However, there are no instances where the deferred revenue would be amortized below the amount that could be potentially refundable pursuant to the terms of the GSK agreement. Further, should GSK exercise its discretionary termination rights, there are no provisions in the GSK agreement that would require the Company to refund payments received relating to its performance of initial discovery activities or milestone payments received under the GSK agreement.

PROMACTA and TPO

In December 2008, the FDA granted accelerated approval of GSK’s PROMACTA ® for the treatment of thrombocytopenia in patients with chronic immune (idiopathic) thrombocytopenic purpura (ITP) who have had

 

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an insufficient response to corticosteroids, immunoglobulins or splenectomy. PROMACTA is the first oral TPO receptor agonist therapy for the treatment of adult patients with chronic ITP. As a result of the FDA’s approval of PROMACTA, the Company will be entitled to receive tiered royalties in the range of 4.7%-9.4% on annual net sales of PROMACTA, net of payments due to Rockefeller as part of a settlement agreement and mutual release the Company entered into on February 11, 2009 with Rockefeller.

In December 2008, the Company entered into an exclusive, worldwide license agreement with SmithKline Beecham Corporation, doing business as GSK. Pursuant to the terms of the license agreement, the Company granted GSK the exclusive right to develop, manufacture and commercialize its LGD-4665 product candidate, as well as all other TPO-related molecules discovered by the Company. LGD-4665 is currently in a Phase II trial for treatment of thrombocytopenia, a condition of low-platelet levels commonly associated with a diverse range of clinical disorders. Under the terms of the license agreement, GSK paid the Company $5.0 million as an upfront license fee which was recognized as revenue in 2008 and agreed to pay the Company up to $158.0 million in development and commercial milestones and a 14.5% royalty on net sales, net of payments due to Rockefeller. In the first year of sales, royalties will be 6.5% on net sales, net of payments due to Rockefeller. GSK has the exclusive right to develop, manufacture and commercialize LGD-4665, as well as other TPO-related molecules discovered by the Company. GSK will direct all product development and commercialization and will be responsible for all costs going forward for development, patent maintenance and prosecution, and commercialization.

Wyeth Collaborations

JAK3 Program

In connection with the completion of the Company’s acquisition of Pharmacopeia, the Company assumed a research and license agreement with Wyeth, acting through its Wyeth Pharmaceuticals Division, providing for the formation of a new alliance based on Pharmacopeia’s Janus Kinase-3, or JAK3, inhibitor program. The alliance’s goal is to identify, develop and commercialize therapeutic products for the treatment of certain immunological conditions in humans.

Each of the companies has certain exclusive rights to develop and commercialize products resulting from the JAK3 program and the alliance. The Company retains the right to develop and commercialize therapeutic products for the treatment of dermatological and ocular diseases employing topical administration, and Wyeth has the right to develop human therapeutic products for all other indications and routes of delivery. Under the terms of the Wyeth agreement, Pharmacopeia received an up-front cash payment and will receive quarterly research funding through December 2009. In addition, the Company may receive up to $175.0 million if Wyeth achieves preclinical and clinical development and regulatory and commercialization milestones, as well as double-digit royalties on the net sales of any products commercialized by Wyeth under the alliance. Each company is responsible for all development, regulatory, manufacturing and commercialization activities for any products it develops and commercializes in its field.

The revenue for this research is recognized on a percentage of completion basis, which is expected to approximate straight-line recognition of revenue over the initial three year term of the alliance. As of December 31, 2008, the Company had deferred revenue of approximately $1.5 million related to Wyeth agreements.

Each of the companies has the right to terminate the Wyeth agreement under certain specified circumstances at any time during the term of the Wyeth agreement. In addition, Wyeth has the right, upon providing the Company six months’ prior written notice, to terminate the research collaboration and/or the Wyeth agreement in its entirety or in part. Such right to termination would not apply to Wyeth’s obligations with respect to any program developed by the collaboration and licensed by Wyeth. Termination will not require the Company to refund to Wyeth any or all of the cash payments described above.

 

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Bazedoxifene Program

Bazedoxifene (VIVIANT) is a product candidate that resulted from another collaboration with Wyeth. Bazedoxifene is a synthetic drug that was specifically designed to reduce the risk of osteoporotic fractures while at the same time protecting breast and uterine tissue. In June 2006, Wyeth submitted an NDA for bazedoxifene to the FDA for the prevention of postmenopausal osteoporosis. The FDA issued an approvable letter for bazedoxifene for this indication in April 2007. Wyeth received a second approvable letter in December 2007 and plans to have further discussions with the FDA to discuss the issues raised for the prevention indication. Wyeth also submitted a second NDA for bazedoxifene in the United States in July 2007 for the treatment of osteoporosis and an MAA to EMEA in September 2007 for the prevention and treatment of osteoporosis. Wyeth received a third approvable letter in the second quarter of 2008 for bazedoxifene for the treatment of osteoporosis. In the letter, the FDA requested information similar to that outlined in its approvable letter for bazedoxifene’s NDA for the prevention of postmenopausal osteoporosis issued in December 2007. This included further analyses concerning the incidence of stroke and venous thrombotic events. Wyeth indicated that it will file a complete response in 2009 and expects the FDA will -convene an advisory committee to review the pending NDAs for both the treatment and prevention of postmenopausal osteoporosis with VIVIANT. In February 2009, VIVIANT received a positive Committee for Medicinal Products for Human Use (CHMP) opinion in Europe for the treatment of postmenopausal osteoporosis in women at increased risk of fracture.

Wyeth is also developing bazedoxifene in combination with PREMARIN (Aprela) as a progesterone-free treatment for menopausal symptoms. Two Phase III studies with bazedoxifene/conjugated estrogens (Aprela), showed reduced number and severity of hot flashes in symptomatic postmenopausal women by up to 80 percent, when compared with placebo. Wyeth expects to file an initial NDA no earlier than the first half of 2010.

The Company previously sold to Royalty Pharma AG, or Royalty Pharma, the rights to a total of 3.0% of net sales of bazedoxifene for a period of ten years following the first commercial sale of each product. After giving effect to the royalty sale, the Company will receive 0.5% of the first $400.0 million in net annual sales. If net annual sales are between $400.0 million and $1.0 billion, the Company will receive a net royalty of 1.5% on the portion of net sales between $400.0 million and $1.0 billion, and if annual sales exceed $1.0 billion, the Company will receive a net royalty of 2.5% on the portion of net sales exceeding $1.0 billion. Additionally, the royalty owed to Royalty Pharma may be reduced by one third if net product sales exceed certain thresholds across all indications.

Pfizer Collaboration

Lasofoxifene (FABLYN) is a product candidate that resulted from the Company’s collaboration with Pfizer. In April 2007, Pfizer announced completion of the Postmenopausal Evaluation and Risk Reduction with lasofoxifene, or PEARL, Phase III study with favorable efficacy and safety. Pfizer submitted an NDA and an MAA for osteoporosis treatment in December 2007 and January 2008, respectively. The FDA Advisory Committee in early September 2008 voted 9-3 in favor of approval of this drug and in January 2009, Pfizer received a complete response letter from the FDA requesting additional information for FABLYN. Pfizer is reviewing the letter and will work with the FDA to determine the appropriate next steps regarding its application. In December 2008 an EU Drug Panel granted a positive opinion for the approval of lasofoxifene in the EU for the treatment of osteoporosis in postmenopausal women at increased risk of fracture. Pfizer has also submitted NDA’s for osteoporosis prevention and vaginal atrophy, and the FDA issued non-approvable letters for both NDA’s.

Under the terms of its agreement with Pfizer, the Company is entitled to receive royalty payments equal to 6% of worldwide net sales of lasofoxifene for any indication. The Company previously sold to Royalty Pharma the rights to a total of 3% of net sales of lasofoxifene for a period of ten years following the first commercial sale of lasofoxifene. Accordingly, the Company will receive approximately 3% of worldwide net annual sales of lasofoxifene.

 

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Cephalon Collaboration

In connection with the Company’s acquisition of Pharmacopeia, the Company assumed a collaboration and license agreement with Cephalon, Inc., or Cephalon, providing for the formation of a new drug discovery, development and commercialization alliance. Under the Cephalon agreement, Pharmacopeia received an up-front, non-refundable payment of $15.0 million in June 2006 to support its research efforts.

Cephalon is responsible for identifying hit and lead compounds, and the Company and Cephalon agreed to work collaboratively to advance the lead compounds to clinical candidates. The Company is principally responsible for medicinal chemistry research and Cephalon provides biology support, including preclinical disease models, as required by the Cephalon agreement. The Company has agreed that, for a specified period, it will not screen its compound library for other collaborators, or for its own account, against any target it works on under the Cephalon agreement.

Upon the nomination of any clinical candidates by the alliance, Cephalon will be primarily responsible for their development and commercialization. The Company will retain an option to develop certain candidates from the alliance, subject to Cephalon’s agreeing to such development. For any preclinical development candidate advanced under the alliance, the developing company will make clinical, regulatory and sales milestone payments to the non-developing company. In addition, the company commercializing any resulting product will pay the non-commercializing company up to double-digit royalties based on the sales level achieved.

As stated above, under the Cephalon agreement, Pharmacopeia received a non-refundable payment of $15.0 million and was principally responsible for performing medicinal chemistry research. The revenue for this research is recognized on a percentage of completion basis. As of December 31, 2008, the Company had deferred revenue of approximately $0.3 million related to the Cephalon agreement. The initial research term of the Cephalon agreement expires in May 2009.

The Company and Cephalon each have the right to terminate the Cephalon agreement under certain specified circumstances at any time during the term of the agreement. In addition, Cephalon has the right to terminate the agreement in its sole discretion, upon ninety days written notice to the Company, during the initial three-year phase of the alliance, which phase may be extended by agreement of the parties. No such termination shall require the Company to refund to Cephalon any or all of the above research and development funding.

Schering-Plough Collaboration

In connection with the completion of the Company’s acquisition of Pharmacopeia, the Company also assumed an amended and restated collaboration and license agreement with N.V. Organon, entered into in February 2007. In November 2007, Organon was acquired by, and is now a part of, Schering-Plough. Under the 2007 Schering-Plough agreement, Pharmacopeia agreed to work collaboratively with Schering-Plough to generate lead compounds at targets in mutual therapeutic areas selected by Schering-Plough and agreed upon by a joint research committee. The purpose of the agreement is to produce development-ready compounds, the potential development of which will be handled primarily by Schering-Plough. The 2007 Schering-Plough agreement provides that the Company will receive up to $4.0 million per year from Schering-Plough in research funding over the remaining portion of the five-year term of the agreement.

Pursuant to the 2007 Schering-Plough agreement the Company has the option to purchase the right to co-develop and co-commercialize certain therapeutic candidates of mutual interest discovered through the alliance. For the therapeutic candidates that the Company does not elect to co-develop and co-commercialize, Schering-Plough will retain exclusive development and commercialization rights, and the Company will receive milestone payments as a result of Schering-Plough’s successful advancement, if any, of each candidate through clinical development. The Company will also receive up to double-digit royalties on net sales, if any, of pharmaceutical products resulting from the collaboration when the lead optimization was conducted by the Company, and lower royalties when the lead optimization was conducted by Schering-Plough.

 

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The Company and Schering-Plough each have the right to terminate the 2007 Schering-Plough agreement at any time during the term of the agreement under certain specified circumstances, and upon other circumstances customary for these types of agreements.

As of December 31, 2008, the Company had deferred revenue of approximately $3.5 million related to Schering-Plough agreement.

Celgene Collaboration

In connection with the acquisition of Pharmacopeia, the Company assumed a research and license agreement (the “Celgene Agreement”) with Celgene Corporation (“Celgene”). As of December 31, 2008, the Company has no further research requirements under the Celgene Agreement. The Company’s relationship with Celgene produced a compound that led to a clinical candidate currently being evaluated for the treatment of fibrotic and inflammatory diseases that entered a Phase I clinical trial in the first quarter of 2008. The Company is entitled to receive payments resulting from the successful achievement by Celgene of clinical milestones, as well as royalties of 2% on net sales of products resulting from the collaboration.

14. Income Taxes

At December 31, 2008, the Company has federal net operating loss carryforwards of $398.4 million and $130.0 million of state net operating loss carryforwards. The Company has $22.4 million of federal research and development credit carryforwards. Federal research and development credit carryforwards of $1.0 million expired at the beginning of 2009 with the remainder expiring through 2028, and the Company has $13.0 million of California and New Jersey research and development credit carryforwards that have no expiration date.

Pursuant to Internal Revenue Code Sections 382 and 383, use of net operating loss and credit carryforwards may be limited if there were changes in ownership of more than 50%. The Company has completed a Section 382 study for Ligand, excluding Glycomed, and has determined that Ligand had an ownership change in 2005 and 2007. As a result of these ownership changes, utilization of Ligand’s net operating losses and credits are subject to limitations under Internal Revenue Code Sections 382 and 383. The information necessary to determine if an ownership change related to Glycomed occurred prior to its acquisition by Ligand is not currently available. Accordingly, such tax net operating loss and credit carryforwards are not reflected in Company’s deferred tax assets. If information becomes available in the future to substantiate the ability to utilize these net operating losses not limited by Sections 382, the Company will record the deferred tax assets at such time. Included in the amounts above are $113.8 million of federal net operating loss carryforwards, $64.2 million of state net operating loss carryforwards and $3.5 million of federal research and development credit carryforwards related to Pharmacopeia. The Company has not completed a 382 study for Pharmacopeia. As such, the utilization of Pharmacopeia’s net operating losses and credits may be subject to limitations under Internal Revenue Code Sections 382 and 383

The Company’s research and development credits pertain to federal, California and New Jersey jurisdictions. These jurisdictions require that the Company create minimum documentation and support. The Company has completed a formal study and believes that it maintains sufficient documentation to support the amounts of the research and development credits.

 

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The components of the income tax benefit for continuing operations are as follows (in thousands):

 

     Years Ended December 31,
     2008    2007     2006

Current Benefit:

       

Federal

   $ 27    $ 16,966     $ 17,122

State

     —        1,743       1,684

Foreign

     28      (12 )    
—  
                     
     55      18,697       18,806
                     

Deferred Benefit:

       

Federal

     —        —         —  

State

     —        —         —  

Foreign

     —        —         —  
                     
   $ 55    $ 18,697     $ 18,806
                     

Significant components of the Company’s deferred tax assets and liabilities as of December 31, 2008 and 2007 are shown below. A valuation allowance has been recognized to fully offset the net deferred tax assets as of December 31, 2008 and 2007 as realization of such assets is not more-likely-than-not.

 

     December 31,  
     2008     2007  
     (in thousands)  

Deferred assets:

    

Net operating loss carryforwards

   $ 141,620     $ 82,117  

Research and AMT credit carryforwards

     35,657       29,709  

Capitalized research and development

     300       856  

Fixed assets and intangibles

     6,255       4,002  

Accrued expenses

     6,042       6,041  

Deferred revenue

     8,823       —    

Litigation settlement reserve

     2,713       —    

Present value of AVINZA royalties

     19,703       26,680  

Organon termination asset

     (22,128 )     (22,292 )

Organon termination liability

     22,128       22,292  

Organon royalty obligation

     818       715  

Deferred sale leaseback

     9,787       10,206  

Other

     5,085       4,390  
                
     236,803       164,716  

Valuation allowance for deferred tax assets

     (236,803 )     (164,716 )
                

Net deferred tax assets

   $ —       $ —    
                

As of December 31, 2008, approximately $6.9 million of the valuation allowance for deferred tax assets related to benefits of stock option deductions which, when recognized, will be allocated directly to paid-in capital. For 2008 and 2007, stock option deductions did not impact the valuation allowance through paid-in capital. For the years ended December 31, 2005, approximately $0.1 million of the change in the valuation allowance is related to benefits of stock option deductions. Additionally, other changes to the valuation allowance allocated directly to accumulated other comprehensive income (loss) are related to unrealized gains and losses on foreign currency transactions of $0.01 million, $0.02 million and $0.4 million for 2008, 2007, and 2006, respectively.

 

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A reconciliation of income tax benefit for continuing operations to the amount computed by applying the statutory federal income tax rate to the loss from continuing operations is summarized as follows (in thousands):

 

     Years Ended December 31,  
     2008     2007     2006  

Amounts computed at statutory federal rate

   $ 33,155     $ 18,174     $ 25,634  

State taxes net of federal benefit

     (2,293 )     1,220       6,500  

Effect of foreign operations

     28       (12 )     —    

Meals & entertainment

     (7 )     (19 )     (113 )

In process R&D from merger

     (24,480 )     —         —    

Stock-based compensation

     (537 )     (910 )     (204 )

Adjustment to NOLs and R&D tax credits

     (678 )           (49,226 )

Federal research and development credits

     (155 )     1,287       353  

Change in valuation allowance

     (5,019 )     (1,043 )     35,862  

Other

     41       —         —    
                        
   $ 55     $ 18,697     $ 18,806  
                        

A reconciliation of income tax benefit (expense) for discontinued operations to the amount computed by applying the statutory federal income tax rate to income from discontinued operations is summarized as follows (in thousands):

 

     Years Ended December 31,  
     2008     2007     2006  

Amounts computed at statutory federal rate

   $ 356     $ (115,333 )   $ (15,087 )

State taxes net of federal benefit

     219       3,109       (1,807 )

Effect of foreign operations

     —         —         (70 )

Stock-based compensation

     —         (40 )     (204 )

Release of FIN 48 liability

     —         398       —    

Change in valuation allowance

     (204 )     89,001       (2,359 )

Other

     21       98       —    
                        
   $ 392     $ (22,767 )   $ (19,527 )
                        

The Company adopted the provisions of FIN 48 on January 1, 2007. FIN 48 clarifies the accounting for income taxes by prescribing a minimum probability threshold that a tax position must meet before a financial statement benefit is recognized. The minimum threshold is defined in FIN 48 as a tax position that is more likely than not to be sustained upon examination by the applicable taxing authority, including resolution of any related appeals or litigation processes, based on the technical merits of the position. As of the date of adoption, the Company’s gross liability for income taxes associated with uncertain tax positions totaled $8.9 million. As a result of the implementation of FIN 48, the Company recognized an increase of $0.4 million to reserve for uncertain tax positions which was recorded as a cumulative effect adjustment to accumulated deficit. The Company’s remaining FIN 48 liabilities are presented net of the deferred tax asset balances on the accompanying consolidated balance sheet.

 

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A reconciliation of the amount of unrecognized tax benefits at December 31, 2008 and 2007 is as follows (in thousands):

 

Balance at December 31, 2006

   $ 8,520  

Additions upon adoption

     398  

Additions based on tax positions related to the current year

     947  

Reductions for tax positions of prior years

     (398 )
        

Balance at December 31, 2007

     9,467  

Additions based on tax positions related to the current year

     322  

Reductions for tax positions of prior years

     (262 )
        

Balance at December 31, 2008

   $ 9,527  
        

Included in the balance of unrecognized tax benefits at December 31, 2008 is $9.5 million of tax benefits that, if recognized would result in adjustments to the related deferred tax assets and valuation allowance and not affect the Company’s effective tax rate.

The Company recognizes interest and penalties related to uncertain tax positions in income tax expense. As of December 31, 2008, accrued interest related to uncertain tax positions is not material.

All of the Company’s tax years from 1991-2007 remain open to examination by the major taxing jurisdictions to which the Company is subject.

15. Summary of Unaudited Quarterly Financial Information

The following is a summary of the unaudited quarterly results of operations for the years ended December 31, 2008 and 2007 (in thousands, except per share amounts).

 

     Quarter ended  
     March 31     June 30     September 30     December 31  

2008

        

Total revenues

   $ 4,874     $ 4,804     $ 5,248     $ 12,389  

Total operating costs and expenses

     17,264       10,928       12,094       86,269  

Income tax benefit (expense)

     1,781       1,030       (2,990 )     234  

Loss from continuing operations

     (9,717 )     (4,889 )     (9,124 )     (73,730 )

Discontinued operations

     5,784       (1,540 )     (9,001 )     4,103  

Net loss

   $ (3,933 )   $ (6,429 )   $ (18,125 )   $ (69,627 )

Basic and diluted per share amounts:

        

Loss from continuing operations

   $ (0.10 )   $ (0.05 )   $ (0.10 )   $ (0.76 )

Discontinued operations

   $ 0.06     $ 0.02     $ (0.09 )   $ 0.04  
                                

Net loss

   $ (0.04 )   $ (0.07 )   $ (0.19 )   $ (0.72 )
                                

Weighted average number of common shares

     95,047       99,056       95,068       96,841  

 

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     Quarter ended  
     March 31     June 30     September 30     December 31  

2007

        

Total revenues

   $ 235     $ 1,410     $ 5,479     $ 5,770  

Total operating costs and expenses

     29,769       16,267       14,694       14,303  

Income tax benefit

     9,194       4,225       2,360       2,918  

Loss from continuing operations

     (16,889 )     (7,686 )     (4,862 )     (5,322 )

Discontinued operations

     291,210       7,867       6,110       11,260  

Net income

   $ 274,321     $ 181     $ 1,248     $ 5,938  

Basic and diluted per share amounts:

        

Loss from continuing operations

   $ (0.17 )   $ (0.08 )   $ (0.05 )   $ (0.06 )

Discontinued operations

     2.89       0.08       0.06       0.12  
                                

Net income

   $ 2.72     $ —       $ 0.01     $ 0.06  
                                

Weighted average number of common shares

     100,686       99,878       96,542       95,223  

16. Sale Leaseback

On October 25, 2006, the Company, along with its wholly-owned subsidiary Nexus, entered into an agreement with Slough for the sale of the Company’s real property located in San Diego, California for a purchase price of $47.6 million. This property, with a net book value of $14.5 million, included one building totaling approximately 82,500 square feet, the land on which the building is situated, and two adjacent vacant lots. As part of the sale transaction, the Company agreed to leaseback the building for a period of 15 years, as further described below. In connection with the sale transaction, on November 6, 2006, the Company also paid off the existing mortgage on the building of $11.6 million. The early payment triggered a prepayment penalty of $0.4 million. The sale transaction closed on November 9, 2006.

Under the terms of the lease, the Company pays a basic annual rent of $3.0 million (subject to an annual fixed percentage increase, as set forth in the agreement), plus a 1% annual management fee, property taxes and other normal and necessary expenses associated with the lease such as utilities, repairs and maintenance, etc. The Company has the right to extend the lease for two five-year terms and will have the first right of refusal to lease, at market rates, any facilities built on the sold lots.

In accordance with SFAS 13, Accounting for Leases , the Company recognized an immediate pre-tax gain on the sale transaction of $3.1 million and deferred a gain of $29.5 million on the sale of the building. The deferred gain is recognized on a straight-line basis over the 15 year term of the lease at a rate of approximately $2.0 million per year. The amount of the deferred gain recognized in 2008, 2007 and 2006 was $2.0 million, $2.0 million and $0.3 million, respectively.

17. Reductions in Workforce

In December 2008, Pharmacopeia announced a reduction in its workforce of thirty positions, twenty-two of which were eliminated effective December 31, 2008 and the remaining eight of which will be eliminated effective June 30, 2009. Accrued severance costs of $0.7 million was included in the accrued restructuring costs as of December 31, 2008. Also included in accrued restructuring costs was a $0.2 million of costs to exit a leased facility which is comprised of the difference between the remaining lease obligations of the abandoned operating leases, which run through the year 2016, and the Company’s estimate of potential future sublease income, discounted to present value.

In December 2007, the Company entered into a plan to eliminate approximately 27 employee positions, across all functional areas, which were no longer deemed necessary in connection with the Company’s ongoing

 

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efforts to be a highly-focused research and development and royalty-driven biotech company. The affected employees were informed of the plan in December 2007 with an effective termination date of December 31, 2007 for the majority of the affected employees. The Company completed the plan by the end of the first quarter of 2008. In connection with the termination plan, the Company recognized expenses of $1.1 million in the fourth quarter of 2007 which was paid in the first quarter of 2008.

In the fourth quarter of 2006, following the sale of the Company’s Oncology Product Line to Eisai, and in the first quarter of 2007, following the sale of AVINZA to King, the Company eliminated nearly 270 employee positions, across all functional areas, which were no longer deemed necessary as a result of the Company’s decision to sell its commercial assets and refocus the Company as a smaller, highly-focused research and development and royalty-driven biotechnology company. As a result, the Company recognized expenses of $11.3 million in 2007 and $2.9 million in 2006.

18. Employment Retention Agreements and Severance Arrangements

In March 2006, the Company entered into letter agreements with approximately 67 key employees, including a number of its executive officers. In September 2006, the Company entered into letter agreements with ten additional employees and modified existing agreements with two employees. These letter agreements provided for certain retention or stay bonus payments to be paid in cash under specified circumstances as an additional incentive to remain employed in good standing with the Company through December 31, 2006. The Compensation Committee of the Board of Directors approved the Company’s expectation of these agreements. In accordance with the SFAS 146, Accounting for Costs Associated with Exit or Disposal Activities , the cost of the plan was ratably accrued over the term of the agreements. Since the retention or stay bonus payments generally vested at the end of 2006 and the total payments to employees was paid in January 2007, the Company recognized $2.6 million of expense under the plan in 2006.

In August 2007, the Compensation Committee of the Company’s Board of Directors approved and ratified change of control agreements with the Company’s executive officers and certain of the Company’s management. In the event the employment of any of the Company’s executive officers is involuntarily terminated in connection with a change of control of the Company, such person, with the exception of the Chief Executive Officer, will receive one year of salary and COBRA health care benefits plus the maximum target bonus for the year. In the event the Chief Executive Officer’s employment is involuntarily terminated in connection with a change of control of the Company, he will receive two years of salary and COBRA health care benefits plus two times the maximum target bonus for the year. The amounts will be payable in a lump sum following the termination of employment. The change of control agreements also accelerate the vesting of all outstanding unvested stock awards and provide that the stock awards may be exercised until nine months after termination or such longer period as may be specified in the applicable stock award agreement, except that no stock award will remain exercisable beyond the original outside expiration date of such stock award.

 

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Item 9. Changes in and Disagreements with Accountants on Accounting and Financial Disclosure

None.

 

Item 9A. Controls and Procedures

(a) Disclosure Controls and Procedures

The Company is required to maintain disclosure controls and procedures that are designed to ensure that information required to be disclosed in its reports under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms, and that such information is accumulated and communicated to management, including the Company’s Chief Executive Officer (CEO) and Chief Financial Officer (CFO) as appropriate, to allow timely decisions regarding required disclosure.

In connection with the preparation of this Form 10-K for the year ended December 31, 2008, management, under the supervision of the CEO and CFO, conducted an evaluation of disclosure controls and procedures. Based on that evaluation, the CEO and CFO concluded that the Company’s disclosure controls and procedures were effective as of December 31, 2008.

(b) Management’s Report on Internal Control over Financial Reporting

Management is responsible for establishing and maintaining adequate internal control over financial reporting for the Company. Internal control over financial reporting is a process to provide reasonable assurance regarding the reliability of the Company’s financial reporting for external purposes in accordance with accounting principles generally accepted in the United States of America. Internal control over financial reporting includes maintaining records that in reasonable detail accurately and fairly reflect the Company’s transactions; providing reasonable assurance that transactions are recorded as necessary for preparation of the Company’s financial statements; providing reasonable assurance that receipts and expenditures of company assets are made in accordance with management authorization; and providing reasonable assurance that unauthorized acquisition, use or disposition of company assets that could have a material effect on the Company’s financial statements would be prevented or detected on a timely basis. Because of its inherent limitations, internal control over financial reporting is not intended to provide absolute assurance that a misstatement of the Company’s financial statements would be prevented or detected.

Management conducted an evaluation of the effectiveness of the Company’s internal control over financial reporting based on the framework in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission. Based on this evaluation, management concluded that the Company’s internal control over financial reporting was effective as of December 31, 2008.

On December 23, 2008, the Company completed the acquisition of Pharmacopeia, Inc. and, as permitted by SEC guidance, the Company excluded from its assessment of the effectiveness of its internal control over financial reporting as of December 31, 2008, the internal control over financial reporting of this entity. Total assets related to Pharmacopeia, Inc. of $36.2 million and no revenues are included in the Company’s consolidated financial statements as of and for the year ended December 31, 2008. The Company plans to integrate Pharmacopeia, Inc.’s historical internal control over financial reporting into its own internal control over financial reporting in 2009. Accordingly, certain changes will be made to the Company’s internal control over financial reporting until such time as this integration is complete.

There were no changes in the Company’s internal control over financial reporting during the quarter ended December 31, 2008, that have materially affected, or are reasonably likely to materially affect, the Company’s internal control over financial reporting. However, we are currently reviewing our controls and procedures based upon the significant reduction in staff as a result of our most recent restructuring.

Grant Thornton LLP, the Company’s independent registered public accountants, has audited the effectiveness of the Company’s internal control over financial reporting as of December 31, 2008, based on the COSO criteria; their report is included in Item 9A.

 

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Report of Independent Registered Public Accounting Firm

Board of Directors and Shareholders

Ligand Pharmaceuticals Incorporated

We have audited Ligand Pharmaceuticals Incorporated’s internal control over financial reporting as of December 31, 2008, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO). Ligand Pharmaceuticals Incorporated’s management is responsible for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting, included in the accompanying Management’s Report on Internal Control Over Financial Reporting. Our responsibility is to express an opinion on Ligand Pharmaceuticals Incorporated’s internal control over financial reporting based on our audit. Our audit of, and opinion on, the Company’s internal control over financial reporting does not include internal control over financial reporting of the wholly owned subsidiary, Pharmacopeia, Inc., whose financial statements reflect total assets and revenues constituting 21 and zero percent, respectively, of the related consolidated financial statement amounts as of and for the year ended December 31, 2008. As indicated in Management’s Report on Internal Control Over Financial Reporting, Pharmacopeia, Inc. was acquired during 2008 and therefore, management’s assertion on the effectiveness of the Company’s internal control over financial reporting excluded internal control over financial reporting of Pharmacopeia, Inc.

We conducted our audit in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether effective internal control over financial reporting was maintained in all material respects. Our audit included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, testing and evaluating the design and operating effectiveness of internal control based on the assessed risk, and performing such other procedures as we considered necessary in the circumstances. We believe that our audit provides a reasonable basis for our opinion.

A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

In our opinion, Ligand Pharmaceuticals Incorporated maintained, in all material respects, effective internal control over financial reporting as of December 31, 2008, based on criteria established in Internal Control—Integrated Framework issued by COSO.

We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States), the consolidated balance sheet of Ligand Pharmaceuticals Incorporated as of December 31, 2008 and the related consolidated statements of operations, stockholders’ equity (deficit) and comprehensive income (loss), and cash flows for the year then ended and our report dated March 13, 2009, expressed an unqualified opinion.

/s/ Grant Thornton LLP

San Diego, California

March 13, 2009

 

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Item 9B. Other Information

None.

Part III

 

Item 10. Directors, Executive Officers and Corporate Governance

Code of Conduct

The Board of Directors has adopted a Code of Conduct and Ethics Policy (“Code of Conduct”) that applies to all officers, directors and employees. The Company will promptly disclose any material amendment or waiver to the Code of Conduct which affects any corporate officer. The Code of Conduct was filed with the SEC as an exhibit to our report on Form 10-K for the year ended December 31, 2003, and can be accessed via our website (http://www.ligand.com), Corporate Overview page. You may also request a free copy by writing to: Investor Relations, Ligand Pharmaceuticals Incorporated, 10275 Science Center Drive, San Diego, CA 92121.

The other information under Item 10 is hereby incorporated by reference from Ligand’s Definitive Proxy Statement to be filed with the Securities and Exchange Commission on or prior to April 29, 2008. See also the identification of the executive officers following Item 4 of this Annual Report on Form 10-K.

 

Item 11. Executive Compensation

Item 11 is hereby incorporated by reference from Ligand’s Definitive Proxy Statement to be filed with the Securities and Exchange Commission on or prior to April 29, 2009.

 

Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters

Item 12 is hereby incorporated by reference from Ligand’s Definitive Proxy Statement to be filed with the Securities and Exchange Commission on or prior to April 29, 2009.

 

Item 13. Certain Relationships and Related Transactions, and Director Independence

Item 13 is hereby incorporated by reference from Ligand’s Definitive Proxy Statement to be filed with the Securities and Exchange Commission on or prior to April 29, 2009.

Item 14. Principal Accountant Fees and Services

Item 14 is hereby incorporated by reference from Ligand’s Definitive Proxy Statement to be filed with the Securities and Exchange Commission on or prior to April 29, 2009.

 

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PART IV

 

Item 15. Exhibits and Financial Statement Schedule

(a) The following documents are included as part of this Annual Report on Form 10-K.

(1) Financial statements

 

Index to Consolidated Financial Statements

 

Report of Independent Registered Public Accounting Firm—Grant Thornton LLP

 

Report of Independent Registered Public Accounting Firm—BDO Seidman, LLP

 

Consolidated Balance Sheets

 

Consolidated Statements of Operations

 

Consolidated Statements of Stockholders’ Equity (Deficit) and Comprehensive Income (Loss)

 

Consolidated Statements of Cash Flows

 

Notes to Consolidated Financial Statements

 

(2) Schedules not included herein have been omitted because they are not applicable or the required information is in the consolidated financial statements or notes thereto.

(3) The following exhibits are filed as part of this Form 10-K and this list includes the Exhibit Index.

 

Exhibit
Number

 

Description

  2.1 (1)   Agreement and Plan of Reorganization dated May 11, 1998, by and among the Company, Knight Acquisition Corp. and Seragen, Inc. (Filed as Exhibit 2.1).
  2.3 (58)   Agreement and Plan of Merger, dated as of September 24, 2008, by and among Ligand Pharmaceuticals Incorporated, Pharmacopeia, Inc., Margaux Acquisition Corp. and Latour Acquisition, LLC. (Exhibit 2.1).
  2.5 (1)   Form of Certificate of Merger for acquisition of Seragen, Inc. (Filed as Exhibit 2.2).
  3.1 (1)   Amended and Restated Certificate of Incorporation of the Company. (Filed as Exhibit 3.2).
  3.2 (1)   Bylaws of the Company, as amended. (Filed as Exhibit 3.3).
  3.3 (2)   Amended Certificate of Designation of Rights, Preferences and Privileges of Series A Participating Preferred Stock of the Company.
  3.4 (20)   Certificate of Amendment of the Amended and Restated Certificate of Incorporation of the Company dated June 14, 2000.
  3.5 (3)   Certificate of Amendment of the Amended and Restated Certificate of Incorporation of the Company dated September 30, 2004.
  3.6 (31)   Amendment to the Bylaws of the Company dated November 13, 2005. (Filed as Exhibit 3.1).
  3.7 (56)   Amendment of Bylaws of the Company dated December 4, 2007. (Filed as Exhibit 3.1).
  4.1 (4)   Specimen stock certificate for shares of Common Stock of the Company.
  4.2 (24)   Pledge Agreement dated November 26, 2002, between Ligand Pharmaceuticals Incorporated and J.P. Morgan Trust Company, National Association. (Filed as Exhibit 4.5).
  4.3 (24)   Control Agreement dated November 26, 2002, among Ligand Pharmaceuticals Incorporated, J.P. Morgan Trust Company, National Association and JP Morgan Chase Bank. (Filed as Exhibit 4.6).
  4.4 (44)   2006 Preferred Shares Rights Agreement, by and between Ligand Pharmaceuticals Incorporated and Mellon Investor Services LLC, dated as of October 13, 2006. (Filed as Exhibit 4.1)

 

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Exhibit
Number

 

Description

10.1 (35)   Second Amendment to Non-Qualified Deferred Compensation Plan.
10.2 (35)   Letter Agreement by and between the Company and Tod G. Mertes dated as of December 8, 2005.
10.3 (4)   Form of Stock Issuance Agreement.
10.30 (4)   Form of Proprietary Information and Inventions Agreement.
10.33 (4)   License Agreement, dated November 14, 1991, between the Company and Rockefeller University (with certain confidential portions omitted).
10.34 (4)   License Agreement and Bailment, dated July 22, 1991, between the Company and the Regents of the University of California (with certain confidential portions omitted).
10.35 (4)   Agreement, dated May 1, 1991, between the Company and Pfizer Inc (with certain confidential portions omitted).
10.38 (4)   License Agreement, dated January 5, 1990, between the Company and the University of North Carolina at Chapel Hill (with certain confidential portions omitted).
10.41 (4)   License Agreement, dated October 1, 1989, between the Company and Institute Pasteur (with certain confidential portions omitted).
10.46 (4)   Form of Indemnification Agreement between the Company and each of its directors.
10.47 (4)   Form of Indemnification Agreement between the Company and each of its officers.
10.58 (4)   Stock Purchase Agreement, dated September 9, 1992, between the Company and Glaxo, Inc.
10.59 (4)   Research and Development Agreement, dated September 9, 1992, between the Company and Glaxo, Inc. (with certain confidential portions omitted).
10.60 (4)   Stock Transfer Agreement, dated September 30, 1992, between the Company and the Rockefeller University.
10.61 (4)   Stock Transfer Agreement, dated September 30, 1992, between the Company and New York University.
10.62 (4)   License Agreement, dated September 30, 1992, between the Company and the Rockefeller University (with certain confidential portions omitted).
10.67 (4)   Letter Agreement, dated September 11, 1992, between the Company and Mr. Paul Maier.
10.73 (14)   Supplementary Agreement, dated October 1, 1993, between the Company and Pfizer, Inc. to Agreement, dated May 1, 1991.
10.78 (15)   Research, Development and License Agreement, dated July 6, 1994, between the Company and Abbott Laboratories (with certain confidential portions omitted). (Filed as Exhibit 10.75).
10.83 (15)   Option Agreement, dated September 2, 1994, between the Company and American Home Products Corporation, as represented by its Wyeth-Ayerst Research Division (with certain confidential portions omitted). (Filed as Exhibit 10.80).
10.93 (5)   Indemnity Agreement, dated June 3, 1995, between the Company, Allergan, Inc. and Allergan Ligand Retinoid Therapeutics, Inc.
10.97 (5)   Research, Development and License Agreement, dated December 29, 1994, between SmithKline Beecham Corporation and the Company (with certain confidential portions omitted).

 

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Exhibit
Number

 

Description

10.98 (5)   Stock and Note Purchase Agreement, dated February 2, 1995, between SmithKline Beecham Corporation, S.R. One, Limited and the Company (with certain confidential portions omitted).
10.140 (18)   Promissory Notes, General Security Agreements and a Credit Terms and Conditions letter dated March 31, 1995, between the Company and Imperial Bank (Filed as Exhibit 10.101).
10.148 (16)   Lease, dated July 6, 1994, between the Company and Chevron/Nexus partnership, First Amendment to lease dated July 6, 1994.
10.149 (17)   Successor Employment Agreement, signed May 1, 1996, between the Company and David E. Robinson.
10.150 (6)   Master Lease Agreement, signed May 30, 1996, between the Company and USL Capital Corporation.
10.151 (17)   Settlement Agreement and Mutual Release of all Claims, signed April 20, 1996, between the Company and Pfizer, Inc. (with certain confidential portions omitted).
10.152 (17)   Letter Amendment to Abbott Agreement, dated March 14, 1996, between the Company and Abbott Laboratories (with certain confidential portions omitted).
10.157 (6)   Master Lease Agreement, signed February 13, 1997, between the Company and Lease Management Services.
10.158 (6)   Lease, dated March 7, 1997, between the Company and Nexus Equity VI LLC.
10.163 (19)   Extension of Master Lease Agreement between Lease Management Services and Ligand Pharmaceuticals dated July 29, 1997.
10.167 (7)   Development and License Agreement, dated November 25, 1997, between the Company and Eli Lilly and Company (with certain confidential portions omitted).
10.168 (7)   Collaboration Agreement, dated November 25, 1997, among the Company, Eli Lilly and Company, and Allergan Ligand Retinoid Therapeutics, Inc. (with certain confidential portions omitted).
10.169 (7)   Option and Wholesale Purchase Agreement, dated November 25, 1997, between the Company and Eli Lilly and Company (with certain confidential portions omitted).
10.171 (7)   First Amendment to Option and Wholesale Purchase Agreement dated February 23, 1998, between the Company and Eli Lilly and Company (with certain confidential portions omitted).
10.172 (7)   Second Amendment to Option and Wholesale Purchase Agreement, dated March 16, 1998, between the Company and Eli Lilly and Company (with certain confidential portions omitted).
10.176 (8)   Secured Promissory Note, dated March 7, 1997, in the face amount of $3,650,000, payable to the Company by Nexus Equity VI LLC. (Filed as Exhibit 10.1).
10.177 (8)   Amended memorandum of Lease effective March 7, 1997, between the Company and Nexus Equity VI LLC. (Filed as Exhibit 10.2).
10.178 (8)   First Amendment to Lease, dated March 7, 1997, between the Company and Nexus Equity VI LLC. (Filed as Exhibit 10.3).
10.179 (8)   First Amendment to Secured Promissory Note, date March 7, 1997, payable to the Nexus Equity VI LLC. (Filed as Exhibit 10.4).
10.184 (9)   Letter agreement, dated May 11, 1998, by and among the Company, Eli Lilly and Company and Seragen, Inc. (Filed as Exhibit 99.6).

 

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Exhibit
Number

 

Description

10.185 (1)   Amendment No. 3 to Option and Wholesale Purchase Agreement, dated May 11, 1998, by and between Eli Lilly and Company and the Company. (Filed as Exhibit 10.6).
10.186 (1)   Agreement, dated May 11, 1998, by and among Eli Lilly and Company, the Company and Seragen, Inc. (Filed as Exhibit 10.7).
10.188 (9)   Settlement Agreement, dated May 1, 1998, by and among Seragen, Inc., Seragen Biopharmaceuticals Ltd./Seragen Biopharmaceutique Ltee, Sofinov Societe Financiere D’Innovation Inc., Societe Innovatech Du Grand Montreal, MDS Health Ventures Inc., Canadian Medical Discoveries Fund Inc., Royal Bank Capital Corporation and Health Care and Biotechnology Venture Fund (Filed as Exhibit 99.2).
10.189 (9)   Accord and Satisfaction Agreement, dated May 11, 1998, by and among Seragen, Inc., Seragen Technology, Inc., Trustees of Boston University, Seragen LLC, Marathon Biopharmaceuticals, LLC, United States Surgical Corporation, Leon C. Hirsch, Turi Josefsen, Gerald S.J. and Loretta P. Cassidy, Reed R. Prior, Jean C. Nichols, Elizabeth C. Chen, Robert W. Crane, Shoreline Pacific Institutional Finance, Lehman Brothers Inc., 520 Commonwealth Avenue Real Estate Corp. and 660 Corporation (Filed as Exhibit 99.4).
10.191 (8)   Letter of Agreement dated September 28, 1998 among the Company, Elan Corporation, plc and Elan International Services, Ltd. (with certain confidential portions omitted), (Filed as Exhibit 10.5).
10.198 (10)   Stock Purchase Agreement by and between the Company and Warner-Lambert Company dated September 1, 1999 (with certain confidential portions omitted). (Filed as Exhibit 10.2).
10.200 (10)   Nonexclusive Sublicense Agreement, effective September 8, 1999, by and among Seragen, Inc., Hoffmann-La Roche Inc. and F. Hoffmann-La Roche Ltd. (with certain confidential portions omitted). (Filed as Exhibit 10.4).
10.203 (10)   License Agreement effective June 30, 1999 by and between the Company and X-Ceptor Therapeutics, Inc. (with certain confidential portions omitted). (Filed as Exhibit 10.7).
10.218 (11)   Royalty Stream Purchase Agreement dated as of December 31, 1999 among Seragen, Inc., the Company, Pharmaceutical Partners, L.L.C., Bioventure Investments, Kft, and Pharmaceutical Royalties, LLC. (with certain confidential portions omitted).
10.220 (12)   Research, Development and License Agreement by and between Organon Company and Ligand Pharmaceuticals Incorporated dated February 11, 2000 (with certain confidential portions omitted).
10.224 (13)   Research, Development and License Agreement by and between Bristol Myers Squibb Company and Ligand Pharmaceuticals Incorporated dated May 19, 2000 (with certain confidential portions omitted).
10.230 (20)   Amended and Restated Registration Rights Agreement, dated as of June 29, 2000 among the Company and certain of its investors.
10.242 (21)   First Addendum to Amended and Restated Registration Rights Agreement dated June 29, 2000, effective as of December 20, 2001.
10.244 (22)   Second Addendum to Amended and Restated Registration Rights Agreement dated June 29, 2000, effective as of March 28, 2002.
10.245 (22)   Purchase Agreement, dated March 6, 2002, between the Company and Pharmaceutical Royalties International (Cayman) Ltd.

 

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Exhibit
Number

 

Description

10.246 (23)   Amended and Restated License Agreement Between The Salk Institute for Biological Studies and the Company (with certain confidential portions omitted).
10.247 (23)   Amendment Number 1 to Purchase Agreement, dated July 29, 2002, between the Company and Pharmaceutical Royalties International (Cayman) Ltd.
10.250 (25)   Amended and Restated License and Supply Agreement, dated December 6, 2002, between the Company, Elan Corporation, plc and Elan Management Limited (with certain confidential portions omitted).
10.252 (25)   Amendment Number 1 to Amended and Restated Registration Rights Agreement, dated November 12, 2002, between the Company and Elan Corporation plc and Elan International Services, Ltd.
10.253 (25)   Second Amendment to Purchase Agreement, dated December 19, 2002, between the Company and Pharmaceuticals Royalties International (Cayman) Ltd.
10.254 (25)   Amendment Number 3 to Purchase Agreement, dated December 30, 2002, between the Company and Pharmaceuticals Royalties International (Cayman) Ltd. (with certain confidential portions omitted).
10.255 (25)   Purchase Agreement, dated December 30, 2002, between the Company and Pharmaceuticals Royalties International (Cayman) Ltd. (with certain confidential portions omitted).
10.256 (26)   Co-Promotion Agreement, dated January 1, 2003, by and between the Company and Organon Pharmaceuticals USA Inc. (with certain confidential portions omitted).
10.258 (27)   Letter Agreement, dated May 20, 2003, between the Company and Tod G. Mertes.
10.259 (27)   Amendment No. 2 to Amended and Restated Registration Rights Agreement, dated June 25, 2003.
10.261 (28)   Letter Agreement, dated July 1, 2003, between the Company and Paul V. Maier.
10.264 (29)   Option Agreement Between Investors Trust & Custodial Services (Ireland) Ltd., as Trustee for Royalty Pharma, Royalty Pharma Finance Trust and the Company, dated October 1, 2003 (with certain confidential portions omitted).
10.265 (29)   Amendment to Purchase Agreement Between Royalty Pharma Finance Trust and the Company, dated October 1, 2003 (with certain confidential portions omitted).
10.267 (36)   2002 Stock Incentive Plan (as amended and restated through March 9, 2006).
10.268 (29)   2002 Employee Stock Purchase Plan, dated July 1, 2002 (as amended through June 30, 2003).
10.269 (29)   Form of Stock Option Agreement.
10.270 (29)   Form of Employee Stock Purchase Plan Stock Purchase Agreement.
10.271 (29)   Form of Automatic Stock Option Agreement.
10.272 (29)   Form of Director Fee Stock Option Agreement.
10.273 (30)   Letter Agreement, dated as of February 26, 2004, between the Company and Martin Meglasson.
10.274 (30)   Adoption Agreement for Smith Barney Inc. Execchoice (R) Nonqualified Deferred Compensation Plan.
10.276 (30)   Manufacturing and Packaging Agreement, dated February 13, 2004 between Cardinal Health PTS, LLC and the Company (with certain confidential portions omitted).
10.279 (32)   Form of Distribution, Storage, Data and Inventory Management Services Agreement.

 

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Exhibit
Number

 

Description

10.280 (32)   Amendment Number 1 to the Option Agreement between Investors Trust & Custodial Services (Ireland) Ltd., solely in its capacity as Trustee for Royalty Pharma, Royalty Pharma Finance Trust and Ligand Pharmaceuticals Incorporated dated November 5, 2004.
10.281 (32)   Amendment to Agreement among Ligand Pharmaceuticals Incorporated, Seragen, Inc. and Eli Lilly and Company dated November 8, 2004.
10.282 (32)   Amendment to Purchase Agreement between Royalty Pharma Finance Trust, Ligand Pharmaceuticals Incorporated & Investors Trust and Custodial Services (Ireland) Ltd., solely in its capacity as Trustee of Royalty Pharma dated November 5, 2004.
10.283 (34)   Form of Management Lockup Agreement.
10.285 (34)   Confidential Interference Settlement Agreement dated March 11, 2005, by and between the Company, SRI International and The Burnham Institute.
10.287 (36)   Amended and Restated Research, Development and License Agreement dated as of December 1, 2005 between the Company and Wyeth (formerly American Home Products Corporation) (with certain confidential portions omitted).
10.288 (33)   Settlement Agreement dated as of December 2, 2005 by and among Ligand Pharmaceuticals Incorporated and Third Point LLC, Third Point Offshore Fund, Ltd., Third Point Partners LP, Third Point Ultra Ltd., Lyxor/Third Point Fund Ltd., and Third Point Partners Qualified LP. (Filed as Exhibit 10.1).
10.289 (36)   Form of Stock Issuance Agreement for non-employee directors.
10.290 (36)   Form of Amended and Restated Director Fee Stock Option Agreement for 2005 award to Alexander Cross.
10.291 (36)   Form of Amended and Restated Director Fee Stock Option Agreement for 2005 award to Henry Blissenbach, John Groom, Irving Johnson, John Kozarich, Daniel Loeb, Carl Peck, Jeffrey Perry, Brigette Roberts and Michael Rocca.
10.292 (37)   Termination and Return of Rights Agreement between Ligand Pharmaceuticals Incorporated and Organon USA Inc. dated as of January 1, 2006
10.292A (38)   Form of Letter Agreement between the Company and certain of its officers dated as of March 1, 2006 (Filed as Exhibit 10.292).
10.293 (40)   First Amendment to the Manufacturing and Packaging Agreement between Cardinal Health PTS, LLC and Ligand Pharmaceuticals Incorporated (with certain confidential portions omitted).
10.294 (42)   Purchase Agreement, by and between Ligand Pharmaceuticals Incorporated, King Pharmaceuticals, Inc. and King Pharmaceuticals Research and Development, Inc., dated as of September 6, 2006.
10.295 (43)   Contract Sales Force Agreement, by and between Ligand Pharmaceuticals Incorporated and King Pharmaceuticals, Inc. dated as of September 6, 2006.
10.296 (42)   Purchase Agreement, by and among Ligand Pharmaceuticals Incorporated, Seragen, Inc., Eisai Inc. and Eisai Co., Ltd., dated as of September 7, 2006.
10.297 (39)   Separation Agreement dated as of July 31, 2006 by and between the Company and David E. Robinson.
10.298 (47)   Offer letter/employment agreement by and between the Company and Henry F. Blissenbach, dated as of August 1, 2006.
10.299 (41)   Form of Letter Agreement (Change of Control Severance Agreement) by and between the Company and certain officers dated as of August 25, 2006.

 

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Exhibit
Number

 

Description

10.300 (41)   Form of Letter Agreement (Ordinary Severance Agreement) by and between the Company and certain officers dated as of August 25, 2006.
10.301 (53)   Stipulation of Settlement by and among Plaintiffs and Ligand Pharmaceuticals, Inc. et al., In re Ligand Pharmaceuticals Inc. Securities Litigation , United States District Court, District of Southern California, dated as of June 28, 2006, approved by Order dated October 16, 2006.
10.302 (53)   Stipulation of Settlement by and among Plaintiffs and Ligand Pharmaceuticals, Inc. et al., In re Ligand Pharmaceuticals Inc. Derivative Litigation , Superior Court of California, County of San Diego, dated as of September 19, 2006, approved by Order dated October 12, 2006.
10.303 (53)   Loan Agreement by and between Ligand Pharmaceuticals Incorporated and King Pharmaceuticals, 303 Inc. dated as of October 12, 2006.
10.304 (49)   Letter Agreement by and between Ligand and King Pharmaceuticals, Inc. effective as of December 29, 2006.
10.305 (49)   Amendment Number 1 to Purchase Agreement, Contract Sales Force Agreement and Confidentiality Agreement by and between Ligand and King Pharmaceuticals, Inc. effective as of November 30, 2006.
10.306 (46)   Purchase Agreement and Escrow Instructions by and between Nexus Equity VI, LLC, a California Limited Liability Company, and Ligand Pharmaceuticals Incorporated, a Delaware Corporation and Slough Estates USA Inc., a Delaware corporation dated October 25, 2006.
10.307 (48)   Amendment No. 1 to the Stockholders Agreement effective as of December 12, 2006, by and among Ligand Pharmaceutical Incorporated and Third Point LLC, Third Point Offshore Fund, Ltd., Third Point Partners LP, Third Point Ultra Ltd., Lyxor/Third Point Fund Ltd., and Third Point Partners Qualified LP.
10.308 (53)   2006 Employee Severance Plan dated as of October 4, 2006.
10.309 (53)   Form of Letter Agreement regarding Change of Control Severance Benefits between the Company and its officers.
10.310 (45)   Form of Letter Agreement by and between the Company and Tod G. Mertes dated as of October 19, 2006.
10.311 (49)   Letter Agreement by and between the Company and John L. Higgins dated as of January 10, 2007.
10.312 (51)   Amendment Number 2 to Purchase Agreement, by and between the Company and King Pharmaceuticals, Inc. effective as of February 26, 2007.
10.313 (52)   Indemnity Fund Agreement.
10.314 (54)   Letter Agreement by and between the Company and John P. Sharp dated as of March 30, 2007. (Filed as Exhibit 10.1).
10.315 (55)   Form of Executive Officer Change in Control Severance Agreement. (Filed as Exhibit 10.1).
10.316 (56)   Third Amendment to the Company’s Nonqualified Deferred Compensation Plan effective as of December 4, 2007. (Filed as Exhibit 10.1).
10.317 (57)   Sublease Agreement between the Company and eBIOSCIENCE, INC., effective as of December 13, 2007. (Filed as Exhibit 10.1).
10.318 (59)   Form of Restricted Stock Unit Grant Notice and Restricted Stock Unit Agreement under the Company’s 2002 Stock Incentive Plan. (Filed as Exhibit 10.318).

 

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Exhibit
Number

 

Description

10.319 (59)   Form of Amendment to Restricted Stock Agreement for executive officers other than Chief Executive Officer. (Filed as Exhibit 10.319).
10.320 (59)   Amendment to Restricted Stock Agreement between the Company and John L. Higgins. (Filed as Exhibit 10.320).
10.321 (60)   Tax Sharing and Indemnification Agreement between Pharmacopeia, Inc. and Pharmacopeia, Inc., dated April 30, 2004 (Filed as Exhibit 10.2).
10.322 (61)   Pharmacopeia Drug Discovery, Inc. Amended and Restated 2004 Stock Incentive Plan. (Filed as Appendix A).
10.323   Pharmacopeia, Inc. 2000 Stock Option Plan.
10.324   Collaboration and License Agreement, dated as of July 9, 2003 and effective August 8, 2003, between Pharmacopeia, Inc. and Schering-Plough Ltd. (with certain confidential portions omitted).
10.325   Collaboration and License Agreement, dated as of July 9, 2003 and effective August 8, 2003, between Pharmacopeia, Inc. and Schering Corporation (with certain confidential portions omitted).
10.326 (62)   Amendment No. 1, dated July 27, 2006, to the Collaboration and License Agreements, effective as of July 9, 2003, between (i) Pharmacopeia, Inc. and Schering Corporation and (ii) Pharmacopeia, Inc. and Schering-Plough Ltd. (Filed as Exhibit 10.1).
10.327   Lease, dated August 20, 2003, between Pharmacopeia, Inc. and Eastpark at 8A (Building 1000).
10.328 (63)   Amendment to Lease, dated September 10, 2007, between Eastpark at 8A and Pharmacopeia, Inc. (Building 1000). (Filed as Exhibit 10.1).
10.329   Lease, dated August 20, 2003, between Pharmacopeia, Inc. and Eastpark at 8A (Building 3000).
10.330 (63)   Amendment to Lease, dated April 18, 2007, between Eastpark at 8A and Pharmacopeia, Inc. (Building 3000). (Filed as Exhibit 10.2).
10.331 (64)   Product Development and Commercialization Agreement among SmithKlineBeecham Corporation, doing business as GlaxoSmithKline, Glaxo Group Limited and Pharmacopeia, Inc., dated as of March 24, 2006 (Filed as Exhibit 10.1).
10.332 (65)   Amendment No. 1, dated August 10, 2006, to the Product Development and Commercialization Agreement among the Company, SmithKlineBeecham Corporation, doing business as GlaxoSmithKline, and Glaxo Group Limited. (Filed as Exhibit 10.2).
10.333 (66)   License Agreement, dated as of March 27, 2006, between Pharmacopeia, Inc. and Bristol-Myers Squibb Company (Filed as Exhibit 10.2).
10.334 (67)   Collaboration and License Agreement between Pharmacopeia, Inc. and Cephalon, Inc., dated May 18, 2006. (Filed as Exhibit 10.1).
10.335 (68)   License Agreement, amended and restated as of July 1, 2003, among The Trustees of Columbia University in the City of New York, Cold Spring Harbor Laboratory and Pharmacopeia, Inc. (Filed as Exhibit 10.2).
10.336 (69)   Form of Purchase Agreement dated July 27, 2005 between Pharmacopeia, Inc. and the Purchasers set forth therein. (Filed as Exhibit 10.1).
10.337 (70)   Form of Indemnity Agreement between Pharmacopeia, Inc. and its directors and executive officers. (Filed as Exhibit 3.3).

 

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Exhibit
Number

 

Description

10.338 (71)   Research and License Agreement, dated December 22, 2006, between Pharmacopeia, Inc. and Wyeth (Filed as Exhibit 10.43).
10.339 (72)   Master Security Agreement, dated December 26, 2006, between Oxford Finance Corporation and Pharmacopeia, Inc. (Filed as Exhibit 10.1)
10.340 (73)   Collaboration and License Agreement, amended and restated effective as of February 8, 2007, between Pharmacopeia, Inc. and N.V. Organon. (Filed as Exhibit 10.1).
10.341 (74)   License Agreement, dated October 11, 2007, between Bristol-Myers Squibb Company and Pharmacopeia, Inc. (Filed as Exhibit 10.45).
10.342 (75)   Discovery Collaboration Agreement, dated October 11, 2007, between Bristol-Myers Squibb Company and Pharmacopeia, Inc. (Filed as Exhibit 10.46).
10.343 (76)   Separation Agreement and General Release, dated May 8, 2008, between Pharmacopeia, Inc. and Leslie Johnston Browne, Ph.D. (Filed as Exhibit 10.1).
10.343 (60)   Contingent Value Rights Agreement, dated December 23, 2008, among the Company, Pharmacopeia, Inc. and Mellon Investor Services LLC. (Filed as Exhibit 10.1).
10.344 (59)   Amended and Restated Severance Plan, dated December 20, 2008, of the Company. (Filed as Exhibit 10.2).
10.345 (77)   Settlement Agreement and Mutual Release of all Claims, by and between the Company and The Salk Institute for Biological Studies, dated as of September 2, 2008 (Filed as 10.316).
10.346   License Agreement, dated of December 17, 2008, between the Company and SmithKline Beecham Corporation, doing business as GlaxoSmithKline (with certain confidential portions omitted).
14.1 (29)   Code of Business Conduct and Ethics.
21.1   Subsidiaries of Registrant (See “Business”).
23.1   Consent of independent registered public accounting firm—Grant Thornton LLP.
23.2   Consent of independent registered public accounting firm—BDO Seidman, LLP.
24.1   Power of Attorney (See page 120).
31.1   Certification by Principal Executive Officer, Pursuant to Rules 13a-14(a) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
31.2   Certification by Principal Financial Officer, Pursuant to Rules 13a-14(a) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
32.1   Certification by Principal Executive Officer, Pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
32.2   Certification by Principal Financial Officer, Pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.

 

(1) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Registration Statement on Form S-4 (No. 333-58823) filed on July 9, 1998.
(2) This exhibit was previously filed as part of and is hereby incorporated by reference to same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended March 31, 1999.
(3) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended September 30, 2004.

 

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(4) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Registration Statement on Form S-1 (No. 33-47257) filed on April 16, 1992 as amended.
(5) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Registration Statement on Form S-1/S-3 (No. 33-87598 and 33-87600) filed on December 20, 1994, as amended.
(6) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Annual Report on Form 10-K for the period ended December 31, 1996.
(7) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Annual Report on Form 10-K for the period ended December 31, 1997.
(8) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended September 30, 1998.
(9) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Current Report on Form 8-K of Seragen, Inc. filed on May 15, 1998.
(10) This exhibit was previously filed as part of and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended September 30, 1999.
(11) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Annual Report on Form 10-K for the period ended December 31, 1999.
(12) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended March 31, 2000.
(13) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2000.
(14) This exhibit was previously filed as part of, and are hereby incorporated by reference to the same numbered exhibit filed with the Company’s Annual Report on Form 10-K for the year ended December 31, 1993.
(15) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended September 30, 1994.
(16) This exhibit was previously filed, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Annual Report on Form 10-K for the year ended December 31, 1995.
(17) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly report on Form 10-Q for the period ended June 30, 1996.
(18) This exhibit was previously filed as part of, and are hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly report on Form 10-Q for the period ended September 30, 1995.
(19) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended June 30, 1997.
(20) This exhibit was previously filed as part of, and are hereby incorporated by reference to the same numbered exhibit filed with the Company’s Annual Report on Form 10-K for the year ended December 31, 2000.
(21) This exhibit was previously filed as part of, and are hereby incorporated by reference to the same numbered exhibit filed with the Company’s Annual Report on Form 10-K for the year ended December 31, 2001.
(22) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended March 31, 2002.
(23) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2002.
(24) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Registration Statement on Form S-3 (No. 333-102483) filed on January 13, 2003, as amended.
(25) This exhibit was previously filed as part of, and are hereby incorporated by reference to the same numbered exhibit filed with the Company’s Annual Report on Form 10-K for the year ended December 31, 2002.
(26) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended March 31, 2003.
(27) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended September 30, 2003.

 

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(28) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended September 30, 2003.
(29) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Annual Report on Form 10-K for the year ended December 31, 2003.
(30) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended March 31, 2004.
(31) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on November 14, 2005.
(32) This exhibit was previously filed as part of, and are hereby incorporated by reference to the same numbered exhibit filed with the Company’s Annual Report on Form 10-K for the year ended December 31, 2004.
(33) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on December 5, 2005.
(34) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended March 31, 2005.
(35) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Current Report on Form 8-K filed on December 14, 2005.
(36) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Registration Statement on Form S-1 (no. 333-131029) filed on January 13, 2006 as amended.
(37) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with an Amendment to the Company’s Registration Statement on Form S-1 (No. 333-1031029) filed on February 10, 2006.
(38) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended March 31, 2006.
(39) This exhibit was previously filed as part of, and is being incorporated by reference to the numbered exhibit filed with the Company’s Current Report Form 8-K filed on August 4, 2006.
(40) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2006.
(41) This exhibit was previously filed as part of, and is being incorporated by reference to the numbered exhibit filed with the Company’s Current Report Form 8-K filed on August 30, 2006.
(42) This exhibit was previously filed as part of, and is being incorporated by reference to the numbered exhibit filed with the Company’s Current Report Form 8-K filed on September 11, 2006.
(43) This exhibit was previously filed as part of, and is being incorporated by reference to the numbered exhibit filed with the Company’s Current Report Form 8-K filed on September 12, 2006.
(44) This exhibit was previously filed as part of, and is being incorporated by reference to the numbered exhibit filed with the Company’s Current Report Form 8-K filed on October 17, 2006.
(45) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on October 20, 2006.
(46) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on October 31, 2006.
(47) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Quarterly Report on Form 10-Q for the period ended September 30, 2006.
(48) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on December 14, 2006.
(49) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on January 5, 2007.
(50) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on January 16, 2007.
(51) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on February 28, 2007.
(52) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on March 5, 2007.

 

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(53) This exhibit was previously filed as part of, and are hereby incorporated by reference to the same numbered exhibit filed with the Company’s Annual Report on Form 10-K for the year ended December 31, 2006.
(54) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on May 4, 2007.
(55) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on August 22, 2007.
(56) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on December 6, 2007.
(57) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on December 19, 2007.
(58) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Company’s Current Report on Form 8-K filed on September 26, 2008.
(59) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Company’s Annual Report on Form 10-K for the period ended December 31, 2007.
(60) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Pharmacopeia, Inc.’s Current Report on Form 8-K filed on May 3, 2004.
(61) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered appendix filed with the Pharmacopeia, Inc.’s Form DEF 14A filed on March 26, 2007.
(62) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Pharmacopeia, Inc.’s Current Report on Form 8-K filed on August 2, 2006.
(63) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Quarterly Report on Form 10-Q for the period ended September 30, 2007.
(64) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Quarterly Report on Form 10-Q for the period ended March 31, 2006.
(65) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Quarterly Report on Form 10-Q for the period ended September 30, 2006.
(66) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Quarterly Report on Form 10-Q for the period ended March 31, 2006.
(67) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Quarterly Report on Form 10-Q for the period ended June 30, 2006.
(68) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Quarterly Report on Form 10-Q for the period ended June 30, 2005.
(69) This exhibit was previously filed as part of, and is hereby incorporated by reference to the numbered exhibit filed with the Pharmacopeia, Inc.’s Current Report on Form 8-K filed on August 2, 2005.
(70) This exhibit was previously filed as part of, and is hereby incorporated by reference to numbered exhibit filed with the Pharmacopeia, Inc.’s Registration Statement on Form 10 (Reg. No. 000-50523).
(71) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Annual Report on Form 10-K for the year ended December 31, 2006.
(72) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Quarterly Report on Form 10-Q for the period ended June 30, 2006.
(73) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Quarterly Report on Form 10-Q for the period ended March 31, 2007.

 

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(74) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Annual Report on Form 10-K for the year ended December 31, 2007.
(75) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Annual Report on Form 10-K for the year ended December 31, 2007.
(76) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Quarterly Report on Form 10-Q for the period ended March 31, 2008.
(77) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same numbered exhibit filed with the Pharmacopeia, Inc.’s Quarterly Report on Form 10-Q for the period ended September 30, 2008.

(4)(d) Financial Statement Schedule

Schedules not included herein have been omitted because they are not applicable or the required information is in the consolidated financial statements or notes thereto.

Schedule II—Valuation and Qualifying Accounts (in thousands)

 

     Balance at
Beginning
of Period
   Charges    Deductions     Other     Balance at
End of
Period

December 31, 2008:

            

Allowance for doubtful accounts and cash discounts

   $ 200    $ —      $ —       $ —       $ 200

Reserve for inventory valuation

     —        —        —         —         —  

Valuation allowance on deferred tax assets

     164,716      14,454      —         57,633       236,803

December 31, 2007:

            

Allowance for doubtful accounts and cash discounts

   $ 530    $ 569    $ 899     $ —       $ 200

Reserve for inventory valuation

     153      14      —         (167 ) (A)     —  

Valuation allowance on deferred tax assets

     253,647      —        88,917       (14 )     164,716

December 31, 2006:

            

Allowance for doubtful accounts and cash discounts

   $ 854    $ 4,167    $ 4,491     $ —       $ 530

Reserve for inventory valuation

     1,745      1,842      2,382       (1,052 ) (B)     153

Valuation allowance on deferred tax assets

     300,630      —        47,363  (C)     380       253,647

 

(A) This reserve was adjusted in connection with the accounting for the sale of the AVINZA Product Line on February 26, 2007.
(B) This reserve was adjusted in connection with the accounting for the sale of the Oncology Product Line on October 25, 2006.
(C) Pursuant to Internal Revenue Code Sections 382 and 383, use of net operating loss and credit carryforwards may be limited if there were changes in ownership of more than 50%. The Company has completed a Section 382 study for Ligand, excluding Glycomed, and has determined that Ligand had an ownership change in 2005 and 2007. As a result of these ownership changes, utilization of Ligand’s net operating losses and credits are subject to limitations under Internal Revenue Code Sections 382 and 383. The information necessary to determine if an ownership change related to Glycomed occurred prior to its acquisition by Ligand is not currently available. Accordingly, this amount includes an adjustment to reduce deferred tax assets and the related valuation allowance for such tax net operating loss and credit carryforwards. If information becomes available in the future to substantiate the amount of these net operating losses and credits not limited by Section 382 and 383, the Company will record the deferred tax assets at such time.

 

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SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

 

LIGAND PHARMACEUTICALS INCORPORATED
By:   /s/    J OHN L. H IGGINS        
  John L. Higgins,
  President and Chief Executive Officer

Date: March 13, 2009

POWER OF ATTORNEY

Know all men by these presents, that each person whose signature appears below constitutes and appoints John L. Higgins or John P. Sharp, his or her attorney-in-fact, with power of substitution in any and all capacities, to sign any amendments to this Annual Report on Form 10-K, and to file the same with exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, hereby ratifying and confirming all that the attorney-in-fact or his or her substitute or substitutes may do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, this report has been signed below by the following persons on behalf of the registrant and in the capacities and on the dates indicated.

 

Signature

  

Title

 

Date

/ S /    J OHN L. H IGGINS        

John L. Higgins

   President, Chief Executive Officer and Director (Principal Executive Officer )   March 13, 2009

/ S /    J OHN P. S HARP        

John P. Sharp

   Vice President, Finance and Chief Financial Officer (Principal Financial and Accounting Officer)   March 13, 2009

/ S /    J ASON M. A RYEH        

Jason M. Aryeh

   Director   March 13, 2009

/ S /    S TEVEN J. B URAKOFF        

Steven J. Burakoff

   Director   March 13, 2009

/ S /    T ODD C. D AVIS        

Todd C. Davis

   Director   March 13, 2009

/ S /    D AVID M. K NOTT        

David M. Knott

   Director   March 13, 2009

/ S /    J OHN W. K OZARICH        

John W. Kozarich

   Director   March 13, 2009

/ S /    B RUCE A. P EACOCK        

Bruce A. Peacock

   Director   March 13, 2009

/ S /    S TEPHEN L. S ABBA        

Stephen L. Sabba

   Director   March 13, 2009

 

120

Exhibit 10.323

PHARMACOPEIA, INC.

2000 STOCK OPTION PLAN

1. PURPOSE OF THE PLAN

The purpose of the Plan is to promote the long term financial success of Pharmacopeia, Inc., its Subsidiaries and Affiliates, and to materially increase shareholder value by: (i) providing performance related incentives that motivate superior performance on the part of the Company’s Employees and Consultants, (ii) providing the Company’s Employees and Consultants with the opportunity to acquire an ownership interest in the Company, and to thereby acquire a greater stake in the Company and a closer identity with it; and (iii) enabling the Company to attract and retain the services of Employees and Consultants of outstanding ability and upon whose judgment, interest and special effort the successful conduct of the Company’s operations is largely dependent.

2. DEFINITIONS

2.1. “Act” means the Securities Exchange Act of 1934, as amended.

2.2. “Affiliate” means any entity other than the Subsidiaries in which the Company has a substantial direct or indirect equity interest, as determined by the Board.

2.3. “Award” means an award of Options, SARs, or Restricted Stock or any combination thereof.

2.4. “Award Share” means any share of Common Stock issued upon the exercise of an Option or SAR, or issued pursuant to an Award of Restricted Stock.

2.5. “Board” means the Board of Directors of the Company.

2.6. “Change of Control” shall mean, following the effective date of this Plan, the occurrence of any of the following events:

2.6.1. the acquisition in one or more transactions by any “Person” (as such term is used for purposes of Section 13(d) or Section 14(d) of the Act”) but excluding, for this purpose, the Company or its Subsidiaries or any employee benefit plan of the Company or its Subsidiaries, of “Beneficial Ownership” (within the meaning of Rule 13d-3 under the Act) of fifty percent (50%) or more of the combined voting power of the Company’s then outstanding voting securities (the “Voting Securities”);


2.6.2. the individuals who, as of the effective date of the Plan, constitute the Board (the “Incumbent Board”) cease for any reason to constitute at least a majority of the Board; provided, however, that if the election, or nomination for election by the Company’s shareholders, of any new director was approved by a vote of at least a majority of the Incumbent Board, such new director shall be considered as a member of the Incumbent Board, and provided further that any reductions in the size of the Board that are instituted voluntarily by the Incumbent Board shall not constitute a Change of Control, and after any such reduction the “Incumbent Board” shall mean the Board as so reduced;

2.6.3. a merger or consolidation involving the Company if the shareholders of the Company, immediately before such merger or consolidation, do not own, directly or indirectly, immediately following such merger or consolidation, more than fifty percent (50%) of the combined voting power of the outstanding Voting Securities of the corporation resulting from such merger or consolidation or a complete liquidation or dissolution of the Company or a sale or other disposition of all or substantially all of the assets of the Company; or

2.6.4. acceptance by shareholders of the Company of shares in a share exchange if the shareholders of the Company, immediately before such share exchange, do not own, directly or indirectly, immediately following such share exchange, more than fifty percent (50%) of the combined voting power of the outstanding Voting Securities of the corporation resulting from such share exchange.

2.7. “Code” means the Internal Revenue Code of 1986, as amended.

2.8. “Committee” means the committee designated by the Board to administer the Plan under Section 4.

2.9. “Common Stock” means the common stock of the Company, or such other class or kind of shares or other securities resulting from the application of Section 9.

2.10. “Company” means Pharmacopeia, Inc., a Delaware corporation, or any successor corporation.

2.11. “Consultant” means a key consultant or advisor to the Company or any of its Subsidiaries or Affiliates who is not an Employee.

2.12. “Disability” means a medically-determinable condition of a permanent nature which, as determined by the Committee, renders a Participant incapable of fulfilling the duties and responsibilities that the Participant was performing for the Company, its Subsidiaries and Affiliates immediately prior to the on-set of such condition.

2.13. “Employee” means an employee of the Company, a Subsidiary or an Affiliate.


2.14. “Fair Market Value” means, on any given date:

2.14.1. if the Common Stock is listed on an established stock exchange or exchanges, the closing price of Common Stock on the principal exchange on which it is traded on such date, or if no sale was made on such date on such principal exchange, on the last preceding day on which the Common Stock was traded;

2.14.2. if the Common Stock is not then listed on an exchange, but is quoted on NASDAQ or a similar quotation system, the closing price per share for the Common Stock as quoted on NASDAQ or similar quotation system on such date;

2.14.3. if the Common Stock is not then listed on an exchange or quoted on NASDAQ or a similar quotation system, the value, as determined in good faith by the Committee.

2.15. “Misconduct” means the commission of any act of fraud, embezzlement or dishonesty by the Participant, any unauthorized use or disclosure by such person of confidential information or trade secrets of the Company (or any Subsidiary or Affiliate), or any other intentional misconduct by such person adversely affecting the business or affairs of the Company (or any Subsidiary or Affiliate) in a material manner. The foregoing definition shall not be deemed to be inclusive of all the acts or omissions which the Company (or any Subsidiary or Affiliate) may consider as grounds for the dismissal or discharge of any Participant or other person in the service of the Company (or any Subsidiary).

2.16. Option” means the right, granted from time to time under the Plan, to purchase Common Stock for a specified period of time at a stated price. Options are not intended to be incentive stock options under Section 422 of the Code.

2.17. “Participant” means an Employee or Consultant who is designated by the Committee as eligible to participate in the Plan and who receives an Award under this Plan.

2.18. “Performance Goal” means a goal that has been established by the Committee and that must be met by the end of a Performance Period. The Committee shall have sole discretion to determine the specific targets within each category of Performance Goals, and whether such Performance Goals have been achieved.

2.19. “Performance Period” means the time period during which Performance Goals must be met.

2.20. “Plan” means the Pharmacopeia, Inc. 2000 Stock Option Plan herein set forth, as amended from time to time.

2.21. “Restricted Stock” means Common Stock awarded by the Committee under Section 8 of the Plan.

2.22. “Restriction Period” means the period during which Restricted Stock awarded under the Plan is subject to forfeiture.


2.23. “SAR” means the right to receive, in cash or in Common Stock, as determined by the Committee, the increase in the Fair Market Value of the Common Stock underlying the SAR from the date of grant to the date of exercise.

2.24. “Subsidiary” means any corporation (other than the Company) in an unbroken chain of corporations beginning with the Company (or any subsequent parent of the Company) if each of the corporations other than the last corporation in the unbroken chain owns stock possessing 50 percent or more of the total combined voting power of all classes of stock in one of the other corporations in such chain.

3. ELIGIBILITY

Any Employee who is not a “covered employee” within the meaning of Section 162(m) of the Code, who is not subject to Section 16 of the Act and who is designated by the Committee as eligible to participate in the Plan, or any Consultant who is designated by the Committee as eligible to participate in the Plan, shall be eligible to receive an Award under the Plan.

4. ADMINISTRATION

4.1. The Committee shall be made up of one or more Board members. Members of the Committee shall be appointed by and hold office at the pleasure of the Board. Committee members may resign at any time by delivering written notice to the Board. Vacancies in the Committee may be filled by the Board.

4.2. The Plan shall be administered by the Committee, which shall have full power to interpret and administer the Plan, and full authority to act in selecting the eligible Employees and Consultants to whom Awards may be granted, in determining the times at which such Awards may be granted, in determining the time and the manner in which Options may be exercised, in determining the amount of Awards that may be granted, in determining the terms and conditions of Awards that may be granted under the Plan and the terms of agreements which will be entered into with Participants (which terms shall not be inconsistent with the terms of the Plan). The Committee also shall have the power to establish different terms and conditions with respect to the granting of the same type of Award to different Participants (regardless of whether the Awards are granted at the same time or at different times).

4.3. The Committee shall have the power to accelerate the exercisability or vesting of any Award, and to determine under Section 10 the effect, if any, of a Change of Control of the Company upon outstanding Awards.

4.4. The Committee shall have the power to adopt regulations for carrying out the Plan and to make changes in such regulations as it shall, from time to time, deem advisable. The Committee shall have the full and final authority in its sole discretion to interpret the provisions of the Plan and to decide all questions of fact arising in the application of the Plan’s provisions, and to make all determinations necessary or advisable for the administration of the Plan. Any interpretation by the Committee of the terms and provisions of the Plan and the administration thereof, and all action taken by the Committee, shall be final, binding, and conclusive for all purposes and upon all Participants.


4.5. Members of the Committee shall receive such compensation for their services as may be determined by the Board. All expenses and liabilities which members of the Committee incur in connection with the administration of the Plan shall be paid by the Company. The Committee may, with the approval of the Board, employ attorneys, consultants, accountants and other service providers. The Committee, the Board, the Company and the Company’s officers shall be entitled to rely upon the advice and opinions of any such person. No member of the Committee or the Board shall be personally liable for any action, determination or interpretation made with respect to the Plan and all members of the Committee and the Board shall be fully protected by the Company in respect of any such action, determination or interpretation in the manner provided in the Company’s bylaws.

5. SHARES OF STOCK SUBJECT TO THE PLAN

5.1. Subject to adjustment as provided in Section 9, the total number of shares of Common Stock available for Awards under the Plan shall be 750,000 shares.

5.2. Any shares issued hereunder may consist, in whole or in part, of authorized and unissued shares or treasury shares. Any shares issued by the Company through the assumption or substitution of outstanding grants from an acquired company shall not reduce the number of shares of Common Stock available for Awards under the Plan. If any shares subject to any Award granted hereunder are forfeited or such Award otherwise terminates without the issuance of such shares or the payment of other consideration in lieu of such shares, the shares subject to such Award, to the extent of any such forfeiture or termination, shall again be available for Awards under the Plan.

6. OPTIONS

The grant of Options shall be subject to the following terms and conditions:

6.1. OPTION GRANTS: Any Option granted under the Plan shall be evidenced by a written agreement executed by the Company and the Participant, which agreement shall conform to the requirements of the Plan and may contain such other provisions not inconsistent with the terms of the Plan as the Committee shall deem advisable.

6.2. NUMBER OF SHARES: The Committee shall specify the number of shares of Common Stock subject to each Option.

6.3. OPTION PRICE: The price per share at which Common Stock may be purchased upon exercise of an Option shall be as determined by the Committee.

6.4. TERM OF OPTION AND VESTING: The Committee shall specify when an Option may be exercisable and the terms and conditions applicable thereto. The term of an Option shall in no event be greater than 10 years. The right to exercise an Option or the underlying shares of Common Stock obtained upon the exercise of an Option may be subject to a vesting schedule or the attainment of Performance Goals as determined by the Committee and set forth in the applicable stock option agreement.


6.5. EXERCISE OF OPTION AND PAYMENT OF OPTION PRICE: An Option may be exercised only for a whole number of shares of Common Stock. The Committee shall establish the time and the manner in which an Option may be exercised. The option price of the shares of Common Stock received upon the exercise of an Option shall be paid in full in cash at the time of the exercise or, with the consent of the Committee, in whole or in part in Common Stock held by the Participant for at least 6 months and valued at their Fair Market Value on the date of exercise. With the consent of the Committee, the option price may also be paid in full by the delivery of a properly executed exercise notice, together with irrevocable instructions to a Company-designated broker to promptly deliver to the Company the amount of sale or loan proceeds required to pay the exercise price.

6.6. TERMINATION BY DEATH OR DISABILITY: If a Participant’s employment with or service to the Company, a Subsidiary or Affiliate terminates by reason of death or as a result of the Participant’s Disability, any unexercised Option granted to the Participant may thereafter be exercised (to the extent such Option was exercisable at the time of the Participant’s death or Disability or to a greater extent permitted by the Committee) by the Participant (or where appropriate, the Participant’s transferee, personal representative, heir or legatee), for, in the case of a Participant’s death, a period of one year (or such other period as specified by the Committee), or in the case of a Participant’s Disability, a period of six months (or such other period as specified by the Committee), from the date of death or termination due to Disability, as applicable, or until the expiration of the stated term of the Option, whichever period is shorter.

6.7. TERMINATION FOR MISCONDUCT: If a Participant’s employment with or service to the Company, a Subsidiary or Affiliate terminates for Misconduct, unless otherwise determined by the Committee, any Options granted to the Participant which are unexercised shall terminate on the date of such termination, or notice of such termination, if earlier.

6.8. RETIREMENT: The Committee shall have the discretion at the time an Option is granted to an Employee to provide that if the Participant’s employment is terminated for reasons other than Misconduct after the Participant has attained age 55 and completed five years of service with the Company, a Subsidiary or Affiliate:

6.8.1. The Option shall continue to vest for up to three years following such termination of employment according to the same vesting schedule as then in effect under the Option, provided that such continued vesting will not extend beyond the original date of expiration of the Option, and/or

6.8.2. The Participant will have a period of up to three years after such termination of employment to exercise the Option, provided such exercise period will not extend beyond the original date of expiration of the Option.


6.9. OTHER TERMINATION: If a Participant’s employment with or service to the Company, a Subsidiary or Affiliate terminates for any reason other than death, Disability, Retirement under Section 6.8 or Misconduct, any unexercised Option granted to the Participant may thereafter be exercised (to the extent such Option was exercisable at the time of the Participant’s termination or to a greater extent permitted by the Committee) by the Participant (or, where appropriate, the Participant’s transferee, personal representative, heir or legatee) for a period of ninety days (or such other period as specified by the Committee), from the date of termination, or until the expiration of the stated term of the Option, whichever period is shorter.

7. STOCK APPRECIATION RIGHTS

The grant of SARs shall be subject to the following terms and conditions:

7.1. GRANT OF SARS: Any SAR granted under the Plan shall be evidenced by a written agreement executed by the Company and the Participant, which agreement shall conform to the requirements of the Plan and may contain such other provisions not inconsistent with the terms of the Plan as the Committee shall deem advisable. The base price of an SAR shall be the Fair Market Value of the Common Stock on the date of grant.

7.2. TANDEM SARS: An SAR granted under the Plan may be granted in tandem with all or a portion of a related Option. An SAR granted in tandem with an Option may be granted either at the time of the grant of the Option or at a time thereafter during the term of the Option and shall be exercisable only to the extent that the related Option is exercisable. The base price of an SAR granted in tandem with an Option shall be the option price under the related Option.

7.3. EXERCISE OF AN SAR: An SAR shall entitle the Participant to surrender unexercised the SAR (or any portion of such SAR) and to receive a payment equal to the excess of the Fair Market Value of the shares of Common Stock covered by the SAR on the date of exercise over the base price of the SAR. Such payment may be in cash, in shares of Common Stock, in shares of Restricted Stock, or any combination thereof, as the Committee shall determine. Upon exercise of an SAR issued in tandem with an Option or lapse thereof, the related Option shall be canceled automatically to the extent of the number of shares of Common Stock covered by such exercise, and such shares shall no longer be available for purchase under the Option. Conversely, if the related Option is exercised, or lapses, as to some or all of the shares of Common Stock covered by the grant, the related SAR, if any, shall be canceled automatically to the extent of the number of shares of Common Stock covered by the Option exercise.

7.4. OTHER APPLICABLE PROVISIONS: SARs shall be subject to the same terms and conditions applicable to Options as stated in sections 6.4, 6.6, 6.7, 6.8 and 6.9.


8. RESTRICTED STOCK

An Award of Restricted Stock is a grant by the Company of a specified number of shares of Common Stock to the Participant, which shares are subject to forfeiture upon the happening of specified events or upon the Participant’s and/or Company’s failure to achieve Performance Goals established by the Committee. A grant of Restricted Stock shall be subject to the following terms and conditions:

8.1. GRANT OF RESTRICTED STOCK AWARD. Any Restricted Stock granted under the Plan shall be evidenced by a written agreement executed by the Company and the Participant, which agreement shall conform to the requirements of the Plan, and shall specify (i) the number of shares of Common Stock subject to the Award, (ii) the Restriction Period applicable to each Award, (iii) the events that will give rise to a forfeiture of the Award, (iv) the Performance Goals, if any, that must be achieved in order for the restriction to be removed from the Award, (v) the extent to which the Participant’s right to receive Common Stock under the Award will lapse if the Performance Goals, if any, are not met, and (vi) whether the Restricted Stock is subject to a vesting schedule. The agreement may contain such other provisions not inconsistent with the terms of the Plan as the Committee shall deem advisable.

8.2. DELIVERY OF RESTRICTED STOCK. Upon determination of the number of shares of Restricted Stock to be granted to the Participant, the Committee shall direct that a certificate or certificates representing the number of shares of Common Stock be issued to the Participant with the Participant designated as the registered owner. The certificate(s) representing such shares shall be legended as to restrictions on the sale, transfer, assignment, or pledge of the Restricted Stock during the Restriction Period and deposited by the Participant, together with a stock power endorsed in blank, with the Company.

8.3. DIVIDEND AND VOTING RIGHTS. Unless otherwise determined by the Committee, during the Restriction Period, the Participant shall have all of the rights of a shareholder, including the right to vote the shares of Restricted Stock and receive dividends and other distributions, provided that distributions in the form of Common Stock shall be subject to the same restrictions as the underlying Restricted Stock.

8.4. RECEIPT OF COMMON STOCK. At the end of the Restriction Period, the Committee shall determine, in light of the terms and conditions set forth in the Restricted Stock agreement, the number of shares of Restricted Stock with respect to which the restrictions imposed hereunder shall lapse. The Restricted Stock with respect to which the restrictions shall lapse shall be converted to unrestricted Common Stock by the removal of the restrictive legends from the Restricted Stock. Thereafter, Common Stock equal to the number of shares of the Restricted Stock with respect to which the restrictions hereunder shall lapse shall be delivered to the Participant (or, where appropriate, the Participant’s legal representative). The Committee may, in its sole discretion, modify or accelerate the vesting and delivery of shares of Restricted Stock.

8.5. TERMINATION OF SERVICE. Unless otherwise determined by the Committee, if a Participant’s employment or service with the Company, a Subsidiary or an Affiliate terminates for any reason, any unvested Restricted Stock shall be forfeited.


9. ADJUSTMENTS UPON CHANGES IN CAPITALIZATION

In the event of a reorganization, recapitalization, stock split, spin-off, split-off, split-up, stock dividend, issuance of stock rights, combination of shares, merger, consolidation or any other change in the corporate structure of the Company affecting Common Stock, or any distribution to shareholders other than a cash dividend, the Committee shall make appropriate adjustment in the number and kind of shares authorized for use under the Plan and any adjustments to outstanding Awards as it determines appropriate. The adjustments to outstanding Awards shall include, but not be limited to, the number of shares covered, the respective prices, limitations, and/or Performance Goals applicable to the outstanding Awards. No fractional shares of Common Stock shall be issued pursuant to such an adjustment. The Fair Market Value of any fractional shares resulting from adjustments pursuant to this Section shall, where appropriate, be paid in cash to the Participant. The determinations and adjustments made by the Committee pursuant to this Section 9 shall be conclusive.

10. CHANGE OF CONTROL OF THE COMPANY

Upon a Change of Control, all outstanding Awards shall be immediately fully vested and exercisable unless such Awards are assumed by the successor corporation, and substituted with Awards involving the common stock of the successor corporation, with the terms and conditions of the substituted Awards being no less favorable than the Awards granted by the Company.

11. EFFECTIVE DATE, TERMINATION AND AMENDMENT

The Plan shall become effective on the date of its adoption by the Board. The Plan shall remain in full force and effect until the earlier of 10 years from the date of its adoption by the Board, or the date it is terminated by the Board. The Board shall have the power to amend, suspend or terminate the Plan at any time, provided that no such amendment shall be made without shareholder approval to the extent such approval is required by any applicable law or the rules of a stock exchange or NASDAQ. Termination of the Plan pursuant to this Section 11 shall not affect Awards outstanding under the Plan at the time of termination.

12. TRANSFERABILITY

Awards may not be pledged, assigned or transferred for any reason during the Participant’s lifetime, and any attempt to do so shall be void and the relevant Award shall be forfeited.

13. GENERAL PROVISIONS

13.1. NO EMPLOYMENT RIGHTS. Nothing contained in the Plan, or any Award granted pursuant to the Plan, shall confer upon any Employee any right with respect to continuance of employment by the Company, a Subsidiary or Affiliate or upon any Consultant any right with respect to continued service for the Company, a Subsidiary or Affiliate nor interfere in any way with the right of the Company, a Subsidiary or Affiliate to terminate the employment or service of any Employee or Consultant at any time.

13.2. TRANSFER OF EMPLOYMENT. For purposes of this Plan, a transfer of employment between the Company and its Subsidiaries and Affiliates shall not be deemed a termination of employment.


13.3. PAYMENT OF TAXES. The Company shall have the power to withhold, or require a Participant to remit to the Company, all taxes required to be paid in connection with any Award, the exercise thereof and the transfer of shares of Common Stock pursuant to this Plan. The Company’s power to withhold a portion of the cash or Common Stock received pursuant to an Award, or require that the Participant remit the applicable taxes shall extend to all applicable Federal, state, local or foreign withholding taxes. In the case of the exercise of Options, the Company shall have the right to retain the shares of Common Stock to be paid pursuant to the exercise of the Option, until the Company determines that the applicable withholding taxes have been satisfied.

13.4. RESTRICTIONS ON SHARES. The Award Shares shall be subject to restrictions on transfer pursuant to applicable securities laws and such other agreements as the Committee shall deem appropriate and shall bear a legend subjecting the Award Shares to those restrictions on transfer in accordance with the applicable Award. The certificates shall also bear a legend referring to any restrictions on transfer arising hereunder or under any other applicable law, regulation, rule or agreement.

13.5. REQUIREMENTS OF LAW. The Plan and each Award under the Plan shall be subject to the requirement that if at any time the Committee shall determine that (a) the listing, registration or qualification of the Award Shares upon any securities exchange or under any state or federal law, (b) the consent or approval of any government regulatory body or (c) an agreement by the recipient of an Award with respect to the disposition of the Award Shares is necessary or desirable as a condition of, or in connection with, the Plan or the granting of such Award or the issue or purchase of the Award Shares thereunder, the Award may not be consummated in whole or in part until such listing, registration, qualification, consent, approval or agreement shall have been effected or obtained free of any conditions not acceptable to the Committee.

13.6. AMENDING OF AWARDS. The Committee may amend any outstanding Awards to the extent it deems appropriate. Such amendment may be made by the Committee without the consent of the Participant, except in the case of amendments adverse to the Participant, in which case the Participant’s consent is required to any such amendment.

13.7. NO SHAREHOLDER RIGHTS. A Participant shall have no rights as a shareholder with respect to shares of Common Stock subject to an Award unless and until certificates for the Award Shares are issued to the Participant.

13.8. CHANGES IN CURRENT LAW. A citation to any law, regulation or rule herein shall be construed to be a citation to the most recent version of, or successor to, any such law, regulation or rule.

13.9. HEADINGS. Section headings are included only for ease of reference. Headings are not intended to constitute substantive provisions of the Plan and shall not be used to interpret the scope of this Plan or the rights or obligations of the Company in any way.


13.9.1. GOVERNING LAW. To the extent that Federal laws do not otherwise control, the Plan and all determinations made and actions taken pursuant hereto shall be governed by the law of the State of Delaware and construed accordingly.

To record the adoption of the Plan, Pharmacopeia, Inc. has caused its authorized officers to affix its corporate name and seal this 11th day of October, 2000.

 

    PHARMACOPEIA, INC.
Attest:      

/s/    Salma Cuadrado

    By:  

/s/    Bruce C. Myers

Exhibit 10.324

 

 

* CERTAIN INFORMATION IN THIS EXHIBIT HAS BEEN OMITTED AND FILED SEPARATELY WITH THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT TO THE OMITTED PORTIONS.

COLLABORATION AND LICENSE AGREEMENT

By and Between

PHARMACOPEIA, INC.

and

SCHERING-PLOUGH LTD.


Table of Contents

 

i


COLLABORATION AND LICENSE AGREEMENT

This COLLABORATION AND LICENSE AGREEMENT (the “Agreement”), dated as of the latest date of signature appearing below (the “Execution Date”) and to be effective as of the Effective Date (as defined below), is made by and among: Pharmacopeia, Inc., a Delaware corporation having its principal place of business at 3000 Eastpark Boulevard, Cranbury, New Jersey 08512, (hereinafter referred to as “Pharmacopeia”); and Schering-Plough Ltd., a Swiss corporation having its principal place of business at Toepferstrasse 5, CH 6004 Lucerne, Switzerland, (hereinafter referred to as “SPL”). Pharmacopeia and SPL are sometimes referred to herein individually as a Party and collectively as the Parties. References to “SPL” and “Pharmacopeia” shall include their respective Affiliates (as hereinafter defined).

WHEREAS, SPL and Pharmacopeia desire to collaborate to design and conduct medicinal chemistry optimization programs against SPL’s biological targets based upon lead compounds selected by SPL; and

WHEREAS, SPL and Pharmacopeia also desire for Pharmacopeia to conduct a separate program to identify new lead compounds by screening certain of its internal compound libraries for activity against biological targets selected by SPL; and

WHEREAS, Pharmacopeia and SPL’s Affiliate Schering Corporation have entered into a collaboration and license agreement relating to the United States of even date herewith; and

WHEREAS, SPL and Pharmacopeia wish to modify and amend certain terms of the existing 1998 Agreements (as defined below) between the Parties related to Optimization Libraries (as defined in the 1998 Agreements);

NOW, THEREFORE, in consideration of the covenants, conditions, and undertakings herein contained, SPL and Pharmacopeia hereby agree as follows:

ARTICLE I

DEFINITIONS

As used in this Agreement, the following capitalized terms, whether used in the singular or plural, shall have the respective meanings set forth below:

1.1 “ Acceptance ” shall mean, with respect to an IND, NDA or HRD submitted by or on behalf of SPL or its Affiliate or Sublicensee, notice by the FDA (or an analogous regulatory authority in another country) that the IND, NDA or HRD has been accepted for review by the FDA (or analogous regulatory authority). In the event that the FDA (or analogous regulatory authority) is not required to provide such a notice of acceptance of an IND, NDA or HRD, then “Acceptance” shall be deemed to occur: (i) in the case of an IND, thirty (30) days following the date of submission, or if previously rejected any resubmission, of such IND; or (ii) in the case of an NDA or HRD, sixty (60) days following the date of submission, or if previously rejected any resubmission, of such NDA or HRD, unless in each case SPL or its Affiliates or Sublicensee receives notice from the FDA (or analogous regulatory authority), during the applicable thirty (30) or sixty (60) day period, that the NDA or HRD is not acceptable for review.

1.2 “ Activity Criteria ” shall mean the threshold criteria to be agreed upon by the Parties for identifying compounds having activity against the relevant Screening Target.

1.3 “ Affiliate ” shall mean any individual or entity directly or indirectly controlling, controlled by or under common control with, a Party to this Agreement. For purposes of this Agreement, the direct or indirect ownership of fifty percent (50%) or more of the outstanding voting securities of an entity, or the right to receive fifty percent (50%) or more of the profits or earnings of an entity shall be deemed to constitute control, or if not meeting the preceding requirements, any company owned or controlled by or owning or controlling Pharmacopeia or SPL at the maximum control or ownership right permitted in a country where such company exists. Such other relationship as in fact results in actual control over the management, business and affairs of an entity shall also be deemed to constitute control. *.

 

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1.4 “ Agreement Compound ” shall mean any Lead Compound or Derivative Compound, as well as *

1.5 “ Agreement Product ” shall mean any product containing an Agreement Compound, including, without limitation, products for the therapeutic or prophylactic treatment or prevention of diseases and conditions in human beings or animals.

1.6 “ Carryover Programs ” shall have the meaning set forth in Section 2.02.

1.7 “ Collaboration ” shall mean the Optimization Programs and Screening Programs to be performed at Pharmacopeia’s facilities by SPL or Pharmacopeia under this Agreement to discover Agreement Compounds for further development by SPL.

1.8 “ Collaboration Committee ” shall have the meaning set forth in Section 3.1.

1.9 “ Collaboration Research Plan ” shall have the meaning set forth in Section 2.1.

1.10 “ Collaboration Target-Specific Technology ” shall mean Collaboration Technology relating to assays, compound screening methods and biological research tools, in each case which are discovered and developed through Collaboration research directed to a specific Target, or a small number of closely related Targets (e.g. a family of biological receptor subtypes), and are not readily applicable to other types of Targets; provided , however , that Collaboration Target-Specific Technology shall not include any rights in or to any Schering Technology (including, without limitation, SPL’s proprietary Targets) or any Agreement Compounds.

1.11 “ Collaboration Technology ” shall mean Collaboration Patent Rights and Collaboration Know-How.

1.11.1 “ Collaboration Patent Rights ” shall mean: (i) all patents and patent applications claiming any invention or discovery made by or on behalf of Pharmacopeia in performance of the Collaboration (including, without limitation, the synthesis and composition of matter of any Agreement Compound, or method of use thereof); and (ii) any divisions, continuations, continuations-in-part, reissues, reexaminations, extensions or other governmental actions which extend any of the subject matter of the patent applications or patents in (i) above, and any substitutions, confirmations, registrations, revalidations, or additions of any of the foregoing, in each case, which is owned or controlled, in whole or part, by license, assignment or otherwise by Pharmacopeia during the term of this Agreement; provided , however , that Collaboration Patent Rights shall not include any patents or patent applications which are Schering Technology or Pharmacopeia Technology.

1.11.2 “ Collaboration Know-How ” shall mean all proprietary ideas, inventions, data, know-how, instructions, processes, formulas, materials, expert opinion and information (including, without limitation, (i) biological, chemical, physical and analytical data and information relating to Agreement Compounds, and (ii) any structure-function data related to Lead Compounds or Derivative Compounds), in each case which is developed by Pharmacopeia in performance of the Collaboration; provided , however , that Collaboration Know-How shall not include Collaboration Patent Rights, Schering Technology or Pharmacopeia Technology.

1.12 “ Combination Product ” shall mean an Agreement Product which comprises two (2) or more active therapeutic ingredients at least one (1) of which is an Agreement Compound.

1.13 “ Derivative Compound ” shall mean any compound derived by Pharmacopeia in the performance of the Collaboration, in each case from one or more Lead Compounds, and having activity against the same Target as such Lead Compound(s). As used herein, a compound shall be deemed to have been “derived from” a Lead Compound if it *

 

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1.14 “ Development Candidate ” shall mean a Lead Compound, Derivative Compound or Schering Derivative which possesses the desirable properties of a therapeutic agent for the prevention or treatment of a clinical condition, in the absence of required safety trials necessary to begin human testing.

1.15 “ Effective Date ” shall have the meaning set forth in Section 2.01.

1.16 “ Excluded Compound ” shall have the meaning set forth in Section 2.9.3.

1.17 “ FDA ” shall mean the United States Food and Drug Administration or any corresponding foreign registration or regulatory authority.

1.18 “ First Commercial Sale ” shall mean, with respect to any Agreement Product, the first sale for end use of such Agreement Product in the Territory after receipt of the requisite Regulatory Approval.

1.19 “ FTE ” shall mean a full-time employee dedicated to the conduct of the Collaboration or, in the case of less than full-time dedication, a full-time equivalent person-year, based on a total of forty-six and one-fourth (46.25) weeks or one thousand eight hundred fifty (1,850) hours per year, of work on or directly related to the Collaboration.

1.20 “ Hit ” shall mean a Pharmacopeia Compound identified by Pharmacopeia during the term and in performance of the Collaboration as meeting the Activity Criteria with respect to the given Screening Target.

1.21 “ HRD ” shall mean a health registration dossier or its equivalent covering an Agreement Product filed in any country outside the United States and which is analogous to an NDA and including, where applicable, applications for pricing, pricing reimbursement approval, labeling and Regulatory Approval.

1.22 “ IND ” shall mean an Investigational New Drug application, as defined in the U.S. Food, Drug and Cosmetic Act and the regulations promulgated thereunder for initiating clinical trials in the United States, or any corresponding foreign application, registration or certification.

1.23 “ Lead Compound ” shall mean any Hit or Schering Compound with respect to which the Parties agree to initiate a program of medicinal chemistry to identify a Development Candidate based upon the structure of such Hit or Schering Compound.

1.24 “ Major Market ” shall mean Japan or any three (3) of the following countries; France, Germany, Italy, Spain or the United Kingdom.

1.25 “ NDA ” shall mean a New Drug Application, Product License Application, or Biologic License Application, as defined in the U.S. Food, Drug and Cosmetics Act and regulations promulgated thereunder, or the equivalent filed with the FDA seeking approval to market and sell an Agreement Product in the United States.

1.26 “ Net Sales ” shall mean, with respect to each country in the Territory, the invoice price billed by SPL or its Affiliates, or their respective Sublicensees, to Third Parties (whether an end-user, a distributor or otherwise) for the sale of Agreement Products, and exclusive of intercompany transfers or sales among SPL, its Affiliates and/or Sublicensees in the Territory, less the reasonable and customary deductions from such gross amounts including: (i) normal and customary trade, cash and quantity discounts, allowances and credits; (ii) credits or allowances actually granted for damaged goods, returns or rejections of Agreement Product and retroactive price reductions; (iii) sales or similar taxes (including duties or other governmental charges levied on, absorbed or otherwise imposed on the sale of Agreement Product including, without limitation, value added taxes or other governmental charges otherwise measured by the billing amount, when included in billing); (iv) freight, postage, shipping, customs duties and insurance charges, when included in billing; (v) charge back payments and rebates granted to managed health care organizations or their agencies, and purchasers and reimbursers or to trade customers, including but not limited to, wholesalers and chain and pharmacy buying groups; (vi) commissions paid to Third Parties other than sales personnel and sale representatives or sales agents; and (vii) rebates (or equivalents thereof) granted to or charged by national, state or local governmental authorities in a country in the Territory. In determining Net Sales of an Agreement Product any of the above discounts shall be accounted for and apportioned based on the list price of each such Agreement Product.

 

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In the event that an Agreement Product is sold in the form of a Combination Product, Net Sales for such Combination Product will be calculated by multiplying actual Net Sales of such Combination Product by the fraction A/(A+B) where: A is the invoice price of the Agreement Product contained in the Combination Product if sold separately by SPL, an Affiliate or Sublicensee; and B is the invoice price of any other active therapeutic ingredients in the Combination Product if sold separately by SPL, an Affiliate or Sublicensee. In the event that the Agreement Product is sold in the form of a Combination Product containing one or more active therapeutic ingredients other than an Agreement Product and one or more such active therapeutic ingredients of the Combination Product are not sold separately, then the above formula shall be modified such that A shall be the fully allocated manufacturing cost to SPL, its Affiliates or Sublicensee of the Agreement Product and B shall be the fully allocated manufacturing cost to SPL, its Affiliate or Sublicensee of any other active therapeutic ingredients in the combination, in each case, determined in accordance with the schedule of fully allocated manufacturing costs set forth in Exhibit C.

1.27 “ Optimization Program ” shall mean a medicinal chemistry research program to discover one or more Development Candidates with respect to a given Target based upon one or more Lead Compounds.

1.28 “ Pharmacopeia Change in Control ” shall mean any of the following: (i) a reorganization, merger or consolidation of Pharmacopeia with a Major Pharmaceutical Company if the shareholders of Pharmacopeia (determined immediately prior to the reorganization, merger or consolidation taking effect) hold, directly or indirectly, less than fifty percent (50%) of the surviving corporation (determined immediately after such reorganization, merger or consolidation takes effect); (ii) an acquisition by a Major Pharmaceutical Company of direct or indirect beneficial ownership of voting stock of Pharmacopeia representing more than fifty percent (50%) of the total current voting power of Pharmacopeia then issued and outstanding; (iii) a sale of all or substantially all the assets of Pharmacopeia’s Drug Discovery division to a Major Pharmaceutical Company; or (iv) a liquidation or dissolution of Pharmacopeia. As used in this Section 1.28, the term “Major Pharmaceutical Company” shall mean any entity (including any corporation, joint venture, partnership or unincorporated entity), as well as any Affiliates or division(s) of such entity, that is engaged in the research, development, manufacturing, registration and/or marketing of drug products that are approved under NDAs, HRDs, ANDAs or Biologics License Applications, having annual sales of pharmaceutical products of *.

1.29 “ Pharmacopeia Compound ” shall mean a compound synthesized and characterized by Pharmacopeia and which is contained in one of Pharmacopeia’s proprietary internal compound libraries.

1.30 “ Pharmacopeia Technology ” shall mean Existing Pharmacopeia Patent Rights, Existing Pharmacopeia Know-How, and Pharmacopeia Improvements.

1.30.1 “ Existing Pharmacopeia Patent Rights ” shall mean (i) all patents and patent applications existing as of the Effective Date that claim the synthesis or composition of matter of a Lead Compound which is a Hit (and/or any other Hits from the same Screening Program as such Lead Compound) or a corresponding Derivative Compound, or the method of use thereof, and (ii) any divisions, continuations, continuations-in-part, reissues, reexaminations, extensions or other governmental actions which extend any of the subject matter of the patent applications or patents in (i) above, and any substitutions, confirmations, registrations, revalidations, or additions of any of the foregoing, in each case, which is owned or controlled, in whole or part, by license, assignment or otherwise by Pharmacopeia during the term of this Agreement, and subject to any limitations and prohibitions of such license or sublicense.

1.30.2 “ Existing Pharmacopeia Know-How ” shall mean all ideas, inventions, data, know-how, instructions, processes, formulas, expert opinion and information, including, without limitation, biological, chemical, physical and analytical data and information, existing as of the Effective Date, owned or controlled in whole or part by Pharmacopeia by license, assignment or otherwise, which is necessary for the discovery, development, manufacture or use of Lead Compounds based on Hits (and/or any other Hits from the same Screening Program as such Lead Compound) or corresponding Derivative Compounds and/or the discovery, development, manufacture, use, sale or commercialization of corresponding Agreement Products, in each case, to the extent Pharmacopeia has the right to license or sublicense the same, and subject to any limitations and prohibitions of such license or sublicense.

 

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1.30.3 “ Pharmacopeia Improvements ” shall mean all patentable inventions conceived and reduced to practice, solely or jointly, by Pharmacopeia or SPL in the conduct of the Collaboration that are within the scope of a claim of an issued patent within the Existing Pharmacopeia Patent Rights (i) which patent issued prior to the Effective Date or (ii) which claim has an effective filing date prior to the Effective Date; provided , however , that Pharmacopeia Improvements shall not include Pharmacopeia Independent Technology (as defined in Section 2.10.1).

1.31 “ Phase III ” shall mean Phase III clinical trials as prescribed by applicable FDA regulations, regardless of whether such trials are conducted in the United States or elsewhere.

1.32 “ Regulatory Approval ” shall mean any applications or approvals, including any INDs, NDAs, supplements, amendments, pre- and post-approvals, marketing authorizations based upon such approvals (including any prerequisite manufacturing approvals or authorizations related thereto) and labeling approval(s), technical, medical and scientific licenses, registrations or authorizations of any national, regional, state or local regulatory agency, department, bureau, commission, council or other governmental entity, necessary for the manufacture, distribution, use, import, export or sale of Agreement Product(s) in the Territory.

1.33 “ Schering Compound ” shall mean a compound which is independently discovered by or on behalf of SPL, without the use of Collaboration Technology or Pharmacopeia Technology as demonstrated by documented evidence created at the time of such discovery, and which is active against a specific Target.

1.34 “ Schering Derivative ” shall mean any compound derived by SPL during the term of the Collaboration or for a period of * the expiration or earlier termination of the Collaboration, in each case from any Derivative Compound(s) or from a Lead Compound which is a Hit, and having as its primary mode of action *As used herein, a compound shall be deemed to have been “derived from” such a Lead Compound or a Derivative Compound if it*.

1.35 “ Schering Technology ” shall mean Schering Patent Rights, Schering Know-How and Schering Improvements.

1.35.1 “ Schering Patent Rights ” shall mean (i) all existing patents and patent applications owned or controlled in whole or in part by SPL or its Affiliates as of the Effective Date (including, without limitation, those which claim the synthesis or composition of matter of a Lead Compound or Derivative Compound, or the method of use thereof, or which relate to any Target or any assay provided by SPL for use in the Collaboration or the corresponding Targets for such assays), (ii) all patents and patent applications claiming any invention or discovery made by or behalf of SPL or its Affiliates, other than in performance of the Collaboration, in connection with the discovery and/or development of any Agreement Compounds and/or Schering Compounds, and/or the development and commercialization of any Agreement Product, and (iii) any divisions, continuations, continuations-in-part, reissues, reexaminations, extensions or other governmental actions which extend any of the subject matter of the patent applications or patents in (i) or (ii) above, and any substitutions, confirmations, registrations, revalidations, or additions of any of the foregoing.

1.35.2 “ Schering Know-How ” shall mean all ideas, inventions, data, know-how, instructions, processes, formulas, materials, expert opinion and information, including, without limitation, biological, chemical, pharmacological, toxicological, pharmaceutical, physical and analytical, clinical, safety, manufacturing and quality control data and information (except for any of the above arising in performance of the Collaboration) owned or controlled in whole or part by SPL by license, assignment or otherwise, which is necessary for the discovery, development, manufacture, use, sale or commercialization of Agreement Products, in each case, to the extent SPL has the right to license or sublicense the same, and subject to any limitations and prohibitions of such license or sublicense; provided , however , that Schering Know-How does not include Schering Patent Rights.

1.35.3 “ Schering Improvements ” shall mean all patentable inventions conceived and reduced to practice solely or jointly by SPL or Pharmacopeia in the conduct of the Collaboration that are within the scope of the claims of any issued patent within the Schering Patent Rights (i) which patent issued prior to the Effective Date or (ii) which claim has an effective filing date prior to the Effective Date.

 

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1.36 “ Screening Program ” shall mean a program to screen Pharmacopeia’s internal compound libraries for activity against one or more Screening Targets for the purpose of identifying Hits.

1.37 “ Screening Target ” shall mean a Target agreed to by the Parties pursuant to Section 2.1.2.

1.38 “ Sublicensee ” shall mean with respect to a particular Agreement Product, a Third Party to whom SPL has granted a sublicense under the applicable Pharmacopeia Technology, Schering Technology or Collaboration Technology to make, use and/or sell such Agreement Product. As used in this Agreement, it is understood that “Sublicensee” shall also include a Third Party or Third Parties to whom SPL has granted the right to distribute such Agreement Product, provided that such Third Party or parties has (have) the primary responsibility for marketing and promotion at its (their) expense of such Agreement Product within the field or territory for which such distribution rights are granted, which marketing and promotional activities are not subsidized directly or indirectly by SPL.

1.39 “ Target ” shall mean a biomolecular entity (including, without limitation, receptors, enzymes, nucleic acids and proteins, and/or fragments thereof) that a small molecule is screened against in order to determine whether the small molecule demonstrates a specific biochemical or pharmaceutical effect.

1.40 “ Territory ” shall mean all of the countries and territories in the world, except for the United States and its territories, possessions and commonwealths.

1.41 “ Third Party ” shall mean any Party other than Pharmacopeia and its Affiliates, SPL and its Affiliates, Schering Corporation and its Affiliates, and their permitted assigns.

1.42 “ 1994 Agreements ” shall have the meaning set forth in Section 11.17.

1.43 “ 1998 Agreements ” shall have the meaning set forth in Section 11.17.

1.44 “ US Agreement ” shall mean that certain Collaboration and License Agreement entered into by and between Pharmacopeia and Schering Corporation of even date herewith.

1.45 “ Valid Claim ” shall mean a composition-of-matter or method-of-use claim of an issued and unexpired patent included within the Collaboration Patent Rights or Pharmacopeia Patent Rights, and in each case which has not been revoked or held unenforceable or invalid by a decision of a court or other governmental agency of competent jurisdiction, unappealable or unappealed within the time allowed for appeal, and which has not been disclaimed, denied or admitted to be invalid or unenforceable through reissue or disclaimer or otherwise.

ARTICLE II

COLLABORATION

2.0 Effective Date; 1998 Agreements .

2.01 Effective Date . SPL and Pharmacopeia have signed this Agreement on the Execution Date as evidence of their mutual desire to establish a collaborative alliance to discover and develop Agreement Products effective against certain Targets. *

2.02 Relationship to 1998 Agreements . As of the Effective Date, all of SPL’s remaining obligations to provide research funding for Pharmacopeia FTEs under Sections 2.4 and 5.2 of the 1998 Agreements, and all of Pharmacopeia’s remaining obligations to provide FTEs under Section 2.5.1 of the 1998 Agreements, shall terminate. In addition, as of the Effective Date, any and all ongoing research programs at Pharmacopeia *shall continue to be performed using the Pharmacopeia FTEs to be provided under this Agreement, as determined by the Collaboration Committee. As of the Effective Date, any and all such ongoing programs (hereinafter “Carryover Programs”) shall be treated under this Agreement as Optimization Programs; provided , however , that notwithstanding

 

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anything herein to the contrary, the provisions of this Agreement related to diligence, milestone payments, royalties, ownership, exclusivity, patent related activities and any and all other rights or obligations with respect to *shall be governed by the terms and conditions of the 1998 Agreements, and SPL shall have no milestone or royalty payment obligations under this Agreement with respect thereto. Except as expressly modified and amended by this Agreement, all other terms and conditions of the 1998 Agreements shall remain in full force and effect.

2.1 Collaboration Research Programs .

2.1.1 Optimization Programs . Within thirty (30) days of the Effective Date, the Collaboration Committee shall agree upon a written overall plan for each of the Optimization Programs to be conducted by the Parties (the “Collaboration Research Plan”). The Collaboration Research Plan shall be periodically revised and updated (at least annually) by the Collaboration Committee during the term of the Collaboration. The Collaboration Research Plan shall set forth the responsibilities of each of the Parties with respect to performance of the Optimization Programs. The Collaboration Committee shall have responsibility for monitoring the performance of Optimization Programs against the current Collaboration Research Plan. Notwithstanding the foregoing, the Parties acknowledge and agree that SPL, in its sole discretion, shall have primary responsibility and decision making authority with respect to the selection of the Targets and Lead Compounds and the specific Optimization Programs to be conducted during the Collaboration; provided that Pharmacopeia shall not be obligated to undertake an Optimization Program for a Target selected by SPL if Pharmacopeia reasonably determines that the performance of an Optimization Program based upon that Target would constitute a breach one or more of Pharmacopeia’s existing contractual obligations to Third Parties; and provided further , that Pharmacopeia’s obligation to undertake such an Optimization Program shall be subject to Section 2.12.

2.1.2 Screening Programs . Within thirty (30) days after the Effective Date, SPL shall notify Pharmacopeia in writing of the identity of*Screening Targets. Such notice shall include the applicable Activity Criteria recommended by SPL for each proposed Screening Target, which Activity Criteria shall constitute Schering Know-How. Such Activity Criteria shall include, without limitation, *Pharmacopeia shall have the right to reject any proposed Targets as Screening Targets if: (i) it has a pre-existing contractual obligation to any Third Party that provides for exclusivity and/or non-compete obligations with respect to such Target; or (ii) Pharmacopeia has previously screened one or more Pharmacopeia Compounds against the same Target and there are less than two million (2,000,000) Pharmacopeia Compounds that have not previously been screened against the Target; or (iii) in accordance with the terms of Section 2.12. In addition, in the event that Pharmacopeia reasonably believes (based upon objective scientific information) that the Activity Criteria recommended by SPL for a proposed Screening Target are not reasonably attainable, then the Collaboration Committee shall promptly meet to agree in good faith upon mutually acceptable Activity Criteria. Pharmacopeia shall promptly notify in writing whether it accepts or rejects each such Target as a Screening Target. SPL shall have the right to propose a replacement Target for each Target rejected by Pharmacopeia, which replacement Target may be accepted or rejected by Pharmacopeia, as described above. The Parties shall use reasonable efforts to agree on *SPL shall propose*additional Targets for acceptance by Pharmacopeia as Screening Targets for Screening Programs. Pharmacopeia shall have the right to accept or reject such Targets, as described above, and the Parties shall use reasonable efforts to agree on *new Screening Targets for Screening Programs to be conducted by Pharmacopeia *To the extent that SPL will be funding *the Parties shall use reasonable efforts to agree upon *new Targets (to be proposed by SPL *as Screening Targets for Screening Programs to be conducted by Pharmacopeia *

2.2 Collaboration Term . The term of the Collaboration shall be *and, unless extended pursuant to Section 2.2.1, or earlier terminated pursuant to Section 2.2.2 or Article X, shall expire on the third anniversary of the Effective Date.

2.2.1 Extension of Collaboration Term . In the event that SPL continues to fund the Collaboration *in accordance with Section 2.5.2, then the Collaboration may be extended for *as provided below. The first *shall be effective upon agreement by SPL *shall be effective upon agreement by SPL *Each of the *shall become effective upon written notice by SPL to Pharmacopeia that it agrees to the *in accordance with Section 2.8.3. * shall be at SPL’s sole discretion and shall be for the purpose of completing any Optimization Programs which are still in progress at the end *The *extension, if any, shall be effective upon written notice by SPL to Pharmacopeia at least * If SPL does not provide such notice, the Collaboration shall expire on *.

 

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2.2.2 Wind Down Period . The parties acknowledge that*of the Collaboration is intended to serve as a wind down period during which any then ongoing Optimization Programs can be completed. Thus, if SPL does not elect to *during the *shall be the wind down period. In the event that SPL is *during *of the Collaboration and SPL does not agree to *during *of the Collaboration based upon one or more *then the Collaboration shall continue for a wind down period of *to enable the Parties to complete and wind down any remaining Optimization Programs then ongoing. SPL’s funding obligations during the *period shall be governed by the terms of Section 2.5.2*, 2.5.4*, or 2.5.3*, as applicable.

2.2.3 Termination of Collaboration Upon Pharmacopeia Change in Control . In the event of a Pharmacopeia Change in Control during the term of the Collaboration, SPL shall have the right, in its discretion, (i) to terminate the Agreement pursuant to Section 10.4.1, below, or (ii) to terminate the Collaboration and not the Agreement upon ninety (90) days written notice to Pharmacopeia after such Change in Control expressly stating its intention to terminate the Collaboration. In the event that SPL elects to terminate the Collaboration and not the Agreement, then (a) SPL will not be obligated to make the payments set forth in Section 5.2 for the period after the effective date of such termination, (b) Pharmacopeia shall not be obligated to conduct any Collaboration research activities after the effective date of such termination, and (c) the remaining terms and conditions of this Agreement, including without limitation the licenses and royalty obligations set forth herein, shall remain in full force and effect until the Agreement expires or is terminated as set forth in Article X, below.

2.2.4 Early Termination of Screening Programs . In the event that Pharmacopeia fails to identify any Hits meeting the applicable Activity Criteria from any of the Screening Programs conducted during * then SPL shall have the right to terminate all further obligations with regard to Screening Programs in *This right shall be exercisable by SPL, in its sole discretion, by providing written notice to that effect to Pharmacopeia within *In the event that the Screening Programs are terminated pursuant to this Section 2.2.4, then Pharmacopeia shall not conduct any further Screening Programs under this Agreement during the remaining term of the Collaboration. In addition, notwithstanding anything herein to the contrary: (i) the Collaboration shall be limited to a total *being a wind down year in which SPL shall only be obligated to fund *chemists, as provided in Section 2.5.2; and (ii) the number of FTEs to be funded during * consisting of*chemistry FTEs and*biology FTEs, to conduct the Optimization Programs *In the event that following such early termination of the Screening Programs by SPL, or during any other wind down period under Section 2.2.2, Pharmacopeia undertakes any new Optimization Programs based upon Lead Compounds which are Schering Compounds (“Wind Down Programs”), then notwithstanding anything herein to the contrary, Pharmacopeia shall be entitled to receive milestone payments with respect to any new Agreement Compounds resulting from such Wind Down Programs under Section 5.4.1(a), but shall not be entitled to receive any royalty payments under Section 5.5 on sales of any Agreement Products containing an Agreement Compound resulting from such Wind Down Programs or with respect to any pharmaceutical products containing a Schering Compound having primary activity against the Target which was the subject of the Wind Down Program.

2.3 Pharmacopeia Responsibilities . Pharmacopeia shall use commercially reasonable efforts to provide:

(i) the number of scientist FTEs agreed to by the Parties, as set forth in Section 2.5, and such additional scientists as may be mutually agreed to in writing by the Parties and paid for by SPL, for performance of the Collaboration during each year of the Collaboration (it being understood and agreed that FTEs provided by Pharmacopeia for the Collaboration under the US Agreement shall also be deemed to be provided to this Collaboration for purposes of determining the number of FTEs provided by Pharmacopeia hereunder);

(ii) research facilities, laboratories and equipment sufficient to enable the Collaboration scientists (including Pharmacopeia employees and one (1) SPL employee to be provided pursuant to Section 2.4(i)) to perform the Collaboration in a fashion similar to the operation of Pharmacopeia’s own operations. The chemistry FTEs shall work in dedicated laboratories at Pharmacopeia’s research facilities in New Jersey; and

(iii) administrative services necessary to conduct the business of the Collaboration in a manner comparable to that of Pharmacopeia ’s own business activities.

 

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It is understood and agreed that, except as may be mutually agreed by the Parties, Pharmacopeia shall not be obligated hereunder to conduct research or development activities in the Collaboration which are outside the scope of the Collaboration Research Plan or the Screening Programs.

2.4 SPL Responsibilities . SPL shall provide research funding for the Collaboration as set forth in Section 5.2 and shall use commercially reasonable efforts to provide:

(i) one scientific director provided by SPL, in combination with Schering Corporation, to work full-time on the Collaboration managing the day-to-day operations of the Collaboration (the “Collaboration Director”);

(ii) additional support for Collaboration research projects, including, without limitation, scientists, facilities and materials to perform biological research to identify Targets, assay development, compound screening, medicinal chemical research and analytical support services; and

(iii) the research materials, procedures and Schering Know-How necessary to conduct the Screening Programs, as provided in Section 2.8.

2.5 Collaboration Staffing .

2.5.1 Pharmacopeia Initial FTE Commitments . During *Pharmacopeia will provide *FTEs, consisting of *synthetic/medicinal chemists *and the remaining *biology FTEs to be allocated, as determined by the Collaboration Committee, between bioassay support for Optimization Programs and performance of Screening Programs. The Parties agree that the Collaboration Committee shall have the right to (i) increase or decrease the total number of FTEs to be provided by Pharmacopeia and funded by SPL during any year of the Collaboration, and/or (ii) to adjust the allocation of the total number of FTEs working on the Collaboration between chemistry and biology FTEs, in each case as necessary to carry out the Collaboration Research Plan; provided , however , that any such adjustments must be agreed upon by the Collaboration Committee in advance in writing, shall not be made more than once in any given quarter, and shall not *or *in any wind down year. Pharmacopeia’s obligation to provide FTEs during*as well as during any extension of the Collaboration pursuant to Section 2.2.1 or wind down period pursuant to Section 2.2.2, shall be determined in accordance with Sections 2.5.2, 2.5.3 or 2.5.4, as applicable. All of the Pharmacopeia chemistry FTEs assigned to work on the Collaboration *On or before the Effective Date, Pharmacopeia will provide to SPL a list individually identifying those Pharmacopeia chemistry FTEs assigned to the Collaboration, which list shall be updated from time to time during the term of the Collaboration as FTEs assigned to work exclusively for the Collaboration are added, removed and/or replaced. During the term of the Collaboration, upon initiating each Optimization Program, Pharmacopeia will also individually identify a biology FTE as the primary contact at Pharmacopeia for the performance of assays and other biology related activities for such Optimization Program, it being understood that such individuals may have responsibility for more than one Optimization Program. It is understood that, in the aggregate, the education, training and experience levels of all Pharmacopeia FTEs assigned to the Collaboration will be reasonably representative of Pharmacopeia employees working on Pharmacopeia’s internal research programs. Within fifteen (15) business days after the Effective Date, Pharmacopeia will provide SPL with: (i) a copy of the Collaboration Business Conduct Policy (as described in Section 7.6) to be observed by all Pharmacopeia FTEs assigned to work on the Collaboration; and (ii) Pharmacopeia’s written representation and warranty that all such FTEs assigned to the Collaboration have read and understand the terms of the Collaboration Business Conduct Policy.

2.5.2 Pharmacopeia FTE Commitments for * In the event that during *the Parties have initiated, or SPL has agreed to initiate, *Optimization Programs *then Pharmacopeia shall continue to provide, and SPL will continue to fund, *FTEs during *If at least *then SPL shall have the right (in its sole discretion) to reduce the number of FTEs to be provided by Pharmacopeia and funded by SPL; provided that the number of Pharmacopeia FTEs to be funded by SPL during the third year of the Collaboration shall be *FTEs; and provided further that all such FTEs shall be chemistry FTEs dedicated to work full time on the Collaboration.

2.5.3 Pharmacopeia FTE Commitments During * If the term of the Collaboration is *pursuant to Section 2.2.1, SPL shall continue to fund and Pharmacopeia shall continue to provide *FTEs during * if applicable. If SPL extends the Collaboration *pursuant to Section 2.2.1, then the level of FTE support to be provided by Pharmacopeia and funded by SPL shall be determined by the Parties based *to be completed during*

 

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2.5.4 Pharmacopeia FTE Commitments * SPL shall have the right (in its sole discretion) to decrease the level of FTE support to be provided by Pharmacopeia and funded by SPL during*as determined pursuant to Section 2.2.2) * provided that the number of Pharmacopeia FTEs to be funded by SPL during *shall be *nd provided further that all such FTEs shall be chemistry FTEs dedicated to work full time on the Collaboration.

2.5.5 SPL FTE Commitments . During the term of the Collaboration SPL shall, in combination with Schering Corporation under the US Agreement, provide a single scientific director as set forth in Section 2.4(i). Such director shall be subject to Pharmacopeia’s confidentiality restrictions such as limited access to laboratories and access only to data that specifically relate to the Collaboration. It is understood that the scientific director shall remain an employee of Schering Corporation, and that SPL shall remain responsible for, and indemnify Pharmacopeia for any claims arising from or relating to, the conduct, activities, salary and benefits of such director, except to the extent caused by the gross negligence or willful misconduct of Pharmacopeia. In addition, SPL shall provide such additional FTEs located at SPL’s research facilities as SPL determines, in its sole discretion, are reasonably necessary to support the ongoing research programs of the Collaboration, including, without limitation, assay development, screening, medicinal chemistry, analytical services and animal testing services.

2.6 Capital Expenditures . In the event that the Parties reasonably determine that one or more Optimization Programs to be performed at Pharmacopeia, as identified in the applicable Collaboration Research Plan, will require capital expenditures to provide Pharmacopeia with access to specialized equipment needed to perform such Optimization Program, SPL shall be responsible (at its expense) for the purchase of such specialized equipment, and for purchasing, or reimbursing Pharmacopeia for the out-of-pocket costs of, any specialized consumables that are uniquely necessary for the proper operation of such specialized equipment. The Parties will make arrangements for the delivery and installation of such specialized equipment at Pharmacopeia’s facilities; provided that the specialized equipment is and shall remain the sole and exclusive property of SPL. Pharmacopeia shall have the right to utilize the specialized equipment in performance of Optimization Programs and shall not use the specialized equipment for any other activities or programs whatsoever. Pharmacopeia shall be responsible (at its own expense) for all routine operating costs incurred in connection with the use of any specialized equipment provided by SPL under this Section 2.6, including without limitation, any utility costs and the costs of reagents, solvents or other supplies necessary for the operation of the specialized equipment. Pharmacopeia shall ensure that all Pharmacopeia employees operating the specialized equipment have been properly trained in its use and shall use the specialized equipment in accordance with the instructions and operating procedures to ensure its proper use. Pharmacopeia shall be responsible (at its expense) for any damage (excluding ordinary wear and tear) to any of SPL’s specialized equipment provided to Pharmacopeia pursuant to this Section 2.6 resulting from Pharmacopeia’s use of the specialized equipment. Upon expiration or earlier termination of the Collaboration, Pharmacopeia shall fully cooperate with SPL to promptly return the specialized equipment to SPL. Alternatively, the Parties may decide to permit Pharmacopeia to retain the specialized equipment following the expiration or termination of the Collaboration, in which case the Parties shall arrange for the purchase and transfer of ownership of the specialized equipment to Pharmacopeia on financial terms to be agreed to by the Parties based upon the then current fair market value of the specialized equipment.

2.7 Record Keeping and Inspection of Records . Each of SPL and Pharmacopeia, and their respective Affiliates, shall maintain records of its Collaboration activities (or cause such records to be maintained) in sufficient detail and in good scientific manner appropriate for patent and regulatory purposes as will properly reflect all work performed and the results achieved in performance of the Collaboration. SPL shall also maintain analogous records of its development activities with respect to Agreement Compounds and Agreement Products. Such records may include books, records, reports, research notes, charts, graphs, comments, computations, analyses, recordings, photographs, computer programs and documentation thereof, computer information storage media, samples of materials and other graphic or written data generated in connection with the Collaboration, including any data required to be maintained pursuant to all requirements of applicable laws, rules and regulations, or as directed by the Collaboration Committee. Pharmacopeia ’s records shall also document by name which individuals assigned to the Collaboration pursuant to Section 2.5 are working on each specific Collaboration research project (identifying the Target(s) involved). During the Collaboration and for five (5) years thereafter, each of SPL and Pharmacopeia shall have the right, upon at least five (5) business days’ prior notice,

 

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to inspect all such records of the other Party (or legible copies thereof) during normal business hours. Each Party’s rights under this Section 2.7 shall be limited to one (1) inspection in any calendar year. In each case, the Party conducting the inspection shall maintain such records and the information disclosed therein in confidence in accordance with Section 7.1, and shall use such information solely for purposes of this Agreement. Upon request and tender of payment for the actual cost in providing copies, Pharmacopeia and/or SPL, as appropriate, shall provide to the requesting Party copies of such records.

2.8 Performance of Screening Programs . With respect to each Screening Target, the Parties agree that promptly following the acceptance by Pharmacopeia of each Screening Target in accordance with Section 2.1.2, SPL will provide Pharmacopeia (free of charge) with reasonable quantities of the Screening Target protein and any of SPL’s other proprietary reagents required to perform assays to identify compounds having activity against such Screening Target. All such proteins and other reagents are and shall remain the property of SPL, shall be used by Pharmacopeia solely in performance of the Screening Program, and shall not be transferred or otherwise made available to any Third Party without SPL’s prior written consent (which consent may be granted or withheld in SPL’s sole discretion.) Upon receipt of such *Pharmacopeia shall use diligent efforts to initiate and conduct a Screening Program to identify Pharmacopeia Compounds having activity against such Screening Target. Such efforts shall include any assay development work or assay modifications necessary to enable Pharmacopeia to perform the relevant assays to determine whether or not the applicable Activity Criteria are met for such Screening Target. Except as otherwise provided in Section 2.6, Pharmacopeia shall be solely responsible *Effective upon acceptance by Pharmacopeia of each Screening Target under Section 2.1.2, Pharmacopeia shall not conduct any screening of Pharmacopeia Compounds, either for itself or for any Third Party, against the same Target as such Screening Target (as determined pursuant to Section 2.11.1) for the period *

2.8.1 Hits . Any Pharmacopeia Compound(s) identified as meeting the Activity Criteria against a Screening Target through screening of the Pharmacopeia Compounds by Pharmacopeia during the term of the Collaboration, shall be designated a Hit. Upon completion by Pharmacopeia of the Screening Program for a given Screening Target, Pharmacopeia shall promptly notify SPL of all Hits identified with respect to that Screening Target, which notice shall identify the Screening Target and the available data generated by Pharmacopeia regarding*but shall not disclose the chemical structure of the Hits, or in the event that no Hits are identified from the Screening Program, Pharmacopeia shall notify SPL to that effect. *information and samples of Hits solely for the purpose of confirming that such Pharmacopeia Compound meets the Activity Criteria for the Screening Target. This will include the performance by SPL of any tests necessary to confirm *SPL agrees, however, not to conduct, or have conducted, *

2.8.2 * Within *SPL shall notify Pharmacopeia in writing of those compounds which SPL has confirmed are Hits *Promptly after receipt of such notice, Pharmacopeia shall disclose to SPL *Upon receipt of the *SPL shall ensure that those employees having access to the*shall only use such information for *

2.8.3 Lead Compounds from Screening Programs . *SPL shall notify Pharmacopeia which (if any) of those confirmed Hits are acceptable to SPL as Lead Compounds for initiation of new Optimization Programs. Following notice from SPL that one or more Hits are acceptable as Lead Compounds, the Parties shall, as soon as reasonably practicable, initiate a new Optimization Program based upon such Lead Compound(s) in accordance with Section 2.9. The Parties acknowledge and agree that if SPL notifies Pharmacopeia that at least one Hit is acceptable to SPL as a Lead Compound for a given Screening Target, then the licenses granted to SPL under Article 4 with respect to such Lead Compound shall also include *The restrictions set forth in Section 2.8.2 regarding disclosure, access and use of structural information with respect to confirmed Hits shall no longer apply following notice of acceptance by SPL of one or more such Hits as a Lead Compound pursuant to this Section 2.8.3. Upon acceptance by SPL of one or more Hits as a Lead Compound pursuant to this Section 2.8.3, the duration of the restriction on screening by Pharmacopeia against the relevant Screening Target, as set forth in the last sentence of Section 2.8, *

2.8.4 Hits Not Accepted by SPL . In the event that SPL does not accept any of the Hits identified by Pharmacopeia with respect to a given Screening Target as Lead Compounds for an Optimization Program, Pharmacopeia shall have the right to *In the event that Pharmacopeia decides to *Following receipt of any*by SPL, the Parties agree that for *

 

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2.9 Performance of Optimization Programs . The first Optimization Programs to be performed under this Agreement are the ongoing research programs for Optimization Libraries (as defined in the 1998 Agreements) listed in Exhibit D, which shall be subject to the terms and conditions of Section 2.0. All new Optimization Programs to be initiated by the Parties after the Effective Date shall be programs based upon Lead Compounds selected under the terms and conditions of this Agreement and Section 2.0 shall not apply to any such new Optimization Programs. It is anticipated that the Parties will generally seek to maintain *ongoing Optimization Programs during each year of the Collaboration in which SPL is funding research at the full level of *FTEs in accordance with Section 2.5; provided , however , that the Parties acknowledge that the actual number of ongoing Optimization Programs at any given time may vary and shall be subject in part to Pharmacopeia’s success in identifying Hits from Screening Programs. If the Parties are unable to maintain *of Optimization Programs based upon Lead Compounds which are Hits from Screening Programs, SPL will use commercially reasonable efforts to approve and initiate new Optimization Programs based upon Lead Compounds which are Schering Compounds as necessary in order maintain a reasonable number of ongoing Optimization Programs based upon the available Pharmacopeia FTEs working on the Collaboration; provided , however , failure by SPL to provide Lead Compounds which are Schering Compounds shall not constitute a breach under this Agreement. If SPL ceases funding the Collaboration at the full level in *in accordance with Sections 2.5.2, 2.5.3 and 2.5.4, then SPL will not be obligated to initiate any new Optimization Programs *The Collaboration Committee shall be responsible for allocation of the FTEs and other resources among the various Optimization Programs selected by SPL. This will include allocation of the medicinal chemistry FTEs, as well as additional FTEs to provide bioassay support, as necessary, for each Optimization Program to generate primary assay data for Lead Compounds and Derivative Compounds. In the event that all FTEs are fully allocated among the various ongoing Optimization Programs, any new Optimization Programs will be initiated as resources become available within the Collaboration, based upon prioritization determined by SPL. Any delay in initiating an Optimization Program based upon a Lead Compound which is a Hit from a Screening Program shall not have any effect on the acceptance of such Hit as a Lead Compound and Pharmacopeia shall not acquire any *.

2.9.1 Preparation of Derivative Compounds . In performing each Optimization Program, Pharmacopeia shall undertake the synthesis of analogs and other Derivative Compounds based upon the relevant Lead Compounds. Pharmacopeia will also conduct primary screening assays of all such Derivative Compounds to determine activity against the applicable Target. Pharmacopeia will provide the Collaboration Committee with regular (at least quarterly) written reports of the data and results generated in performance of each Optimization Program. Such reports will identify the chemical structure of any and all Derivative Compounds prepared by Pharmacopeia in performance of the Optimization Program (whether or not such compounds are identified as active against the Target), and all test data with respect thereto.

2.9.2 *

2.9.3 * Notwithstanding the provisions of Section 2.9.2, in the event

* 2.9.4 Leads Based Upon Schering Compounds . SPL shall not be obligated to disclose the structure of any Schering Compound(s) proposed as Lead Compounds unless and until Pharmacopeia has agreed, pursuant to Section 2.1.1, to conduct an Optimization Program against the relevant Target. Upon Pharmacopeia’s agreement to conduct an Optimization Program based upon one or more Lead Compounds which are Schering Compounds, SPL shall disclose to Pharmacopeia the structure of such Schering Compounds. Effective upon the date Pharmacopeia agrees to perform an Optimization Program based upon one or more Lead Compounds which are Schering Compounds, *for the period extending from

* 2.10 Pharmacopeia Independent Research Activities .

2.10.1 Activities Outside the Collaboration . The Parties acknowledge that during and after the term of the Collaboration Pharmacopeia may (either alone or in collaboration with one or more Third Parties) perform independent research and development activities with respect to Targets (including, without limitation, to identify, develop and commercialize products), which activities are not within the scope of this Agreement; provided that Pharmacopeia shall not use any Schering Technology, and except as otherwise expressly set forth in this Agreement shall not use any Collaboration Technology, in connection with any such independent research and development activities.

 

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Any data, information, materials, compounds, products or other technology resulting from such independent research and development activities is the property of Pharmacopeia (“Pharmacopeia Independent Technology”). The Parties further acknowledge that Pharmacopeia Independent Technology may include technology independently acquired, discovered or developed by Pharmacopeia (as demonstrated by documented evidence created at the time of such acquisition, discovery or development) and which coincidentally is substantially the same as technology within the scope of Collaboration Technology and/or Schering Technology. SPL shall have no rights or licenses whatsoever to any Pharmacopeia Independent Technology.

2.11 SPL’s Screening Programs . The Parties acknowledge that SPL shall have the right to conduct its own independent screening programs against any and all Targets, and that except as expressly set forth in this Section 2.11, *resulting from such independent screening programs. SPL shall have the right *The Parties acknowledge and agree that any pharmaceutical products discovered, developed and commercialized as a result of *are and shall be treated as Agreement Products and shall be subject to *but shall not be subject to *

2.11.1 Differentiation of Targets . A Target will encompass *

2.12 Third Party Patents . The Parties acknowledge and agree that Pharmacopeia shall have the right to reject and shall not be obligated to undertake any Screening Program or Optimization Program, or any new research activities in connection with an ongoing Screening Program or Optimization Program, pursuant to this Agreement if Pharmacopeia reasonably determines, in good faith, that such program or activities cannot be performed without infringing an issued US patent held by a Third Party. It is further understood and agreed that, unless SPL obtains a license for Pharmacopeia, or grants Pharmacopeia a sublicense under a license held by SPL, to conduct such program or research activities, Pharmacopeia’s failure to conduct such program or research activities shall not constitute a breach of this Agreement. Pharmacopeia shall promptly inform SPL in the event that Pharmacopeia determines in accordance with this Section 2.12 that it will be unable to undertake any proposed Screening Program, Optimization Program or research activities due to Third Party patents. *

ARTICLE III

COLLABORATION MANAGEMENT

3.1 Collaboration Committee . The Parties shall establish a Collaboration Committee to oversee, review and coordinate the conduct of the Collaboration. The Collaboration Committee shall be comprised of three (3) representatives from each of SPL and Pharmacopeia, or such other equal number of representatives as the Parties may agree, each Party’s members selected by that Party. Each of Pharmacopeia and SPL may replace its Collaboration Committee representatives at any time upon written notice to the other Party. The Collaboration Committee shall be chaired by the Collaboration Director appointed by SPL, unless otherwise agreed by the Parties. From time to time the Collaboration Committee may establish various subcommittees, constituted as agreed by the Collaboration Committee, to oversee particular projects or activities within the Collaboration.

3.2 Collaboration Committee Meetings . During the term of the Collaboration, including as it may be extended, the Collaboration Committee shall meet at least four (4) times per year, or more often as agreed by the Parties, at such locations as the Parties shall agree. At such meetings the Collaboration Committee’s responsibilities will include: (i) formulating and reviewing the Collaboration objectives with respect to each Optimization Program; (ii) monitoring the progress of the Collaboration toward those objectives; (iii) evaluating Hits identified by Pharmacopeia from Screening Programs; (iv) initially reviewing recommendations by Pharmacopeia to SPL for Hits proposed to be accepted as Lead Compounds for new Optimization Programs; and (v) taking such other actions as may be specified under this Agreement or which the Parties deem appropriate. The Collaboration Committee may designate a patent committee comprised of employees or representatives of the Parties to oversee the patent prosecution and/or enforcement activities described in Article VI, and to facilitate communication and agreement between the Parties regarding inventorship of inventions made in the Collaboration and the classification of such inventions (e.g., as Schering Improvements, Pharmacopeia Improvements, Collaboration Technology, etc.). Additional non-voting representatives or consultants from either Party may from time to time be invited by SPL or Pharmacopeia to attend and participate in Collaboration Committee meetings (e.g., to evaluate and advise on business or scientific issues) subject to compliance with the confidentiality provisions of Section 7.1. Each Party shall be responsible for its own expenses in connection with the Collaboration Committee.

 

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3.3 Collaboration Committee Decisions . Decisions of the Collaboration Committee shall be based upon the consensus of all the members. In the event that the Collaboration Committee cannot or does not, after good faith efforts, reach agreement on an issue, such issue shall be referred to the President of SPL ’s Affiliate, the Schering-Plough Research Institute (“SPRI”), and the President and Chief Operating Officer of Pharmacopeia Drug Discovery for resolution. In the event that these officers are unable to resolve the issue within fifteen (15) business days after submission of the issue to them, then the unresolved issue may be submitted by either Party to binding arbitration pursuant to Section 11.3 of this Agreement, except that the decision shall be made by one (1) arbitrator with expertise in pharmaceutical product development, and the decision of the arbitrator shall be rendered within six (6) months of initiation of the arbitration. During the pendency of any such arbitration proceedings, the Parties shall proceed with performance of the Collaboration following the course of conduct determined by SPL; provided , however , that notwithstanding the foregoing, Pharmacopeia shall not be obligated to (i) perform any action that would violate its obligations to any Third Party or contravene Section 2.12, (ii) spend or forego receiving any amounts of money (except as necessary in connection with the fulfillment of Pharmacopeia’s responsibilities under Section 2.3), or (iii) knowingly prepare or deliver to SPL any compounds previously licensed to any Third Party. Notwithstanding the foregoing, SPL, in its sole discretion, shall have complete and final control over SPL’s research, development and commercialization of Schering Compounds, Agreement Compounds and/or Agreement Product(s) in accordance with the terms and conditions of this Agreement.

3.4 Development Status; Notice of Sale of Agreement Products . During the term of this Agreement, SPL shall provide Pharmacopeia written annual reports within thirty (30) days after the first and each subsequent anniversary of the Effective Date, which reports shall provide: (i) a brief report summarizing the development status of each Lead Compound and/or Development Candidate under development at SPL; (ii) the status of all patent applications claiming any Library Compounds or Derivative Compounds, and (iii) copies of all such patent applications which have published during the relevant twelve (12) month period and were not previously provided to Pharmacopeia. Such reports shall contain information sufficient to allow Pharmacopeia to monitor the status of SPL’s efforts with respect to the accomplishment of the milestones set forth in Section 5.3; provided , however , that nothing hereunder shall be construed as requiring SPL to provide Pharmacopeia with any specific research data or results, including, without limitation, information relating to Targets or data obtained from screening programs being conducted at SPL. Until the First Commercial Sale of each Agreement Product by or on behalf of SPL hereunder, SPL shall keep Pharmacopeia reasonably informed as to the status of the pre-clinical, clinical and commercial development of such Agreement Product by providing Pharmacopeia with annual written reports summarizing such activities with respect to each potential Agreement Product under development during the term of this Agreement. Within thirty (30) days of the First Commercial Sale of any Agreement Product, SPL shall give Pharmacopeia written notice thereof, which notice shall describe the relevant Agreement Product, identify the active ingredients in such Agreement Product, and identify the specific Target(s) which led to the development of such Agreement Product.

3.5 Diligence . The Parties acknowledge and agree that all business decisions regarding research, development and commercialization of Agreement Products (including, without limitation, decisions relating to the development and manufacture of Agreement Compounds, or to the design, development, manufacture, sale, price, distribution, marketing and promotion of Agreement Products under this Agreement) and the decision whether to develop (or cease developing) a particular Agreement Compound, or to develop and commercialize (or cease developing and commercializing) a particular Agreement Product, shall be within the sole discretion of SPL. SPL shall use reasonable good faith efforts to discover and develop Agreement Compounds, and to discover, develop and commercialize Agreement Products; provided , however , that SPL shall have no quotas or other minimum diligence obligations with regard to number of Agreement Compounds and Agreement Products to be developed and commercialized hereunder. Such decision making and/or reasonable good faith efforts shall be expended by SPL, as determined in its reasonable commercial judgement, based upon the facts and circumstances in existence and reasonably available to SPL at that time, and shall be exercised in a manner consistent with the discovery, development and commercialization of SPL’s other products of comparable commercial value, potential and stage of development. All of SPL’s diligence obligations hereunder are expressly conditioned upon the continuing absence of any adverse condition or event which warrants a delay in commercialization of an Agreement Product including, but not limited to, an adverse condition or event relating to the safety or efficacy of the Agreement Product or unfavorable

 

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pricing, pricing reimbursement, labeling or lack of Regulatory Approval, and SPL shall have no obligation to develop or market any such Agreement Product so long as in SPL’s opinion any such condition or event exists; provided that SPL shall use commercially reasonable efforts to overcome any unfavorable pricing or pricing reimbursement with respect to Agreement Products being commercialized under this Agreement. The Parties acknowledge and agree that none of the diligence obligations in this Section 3.5 shall apply to any Schering Compounds, the discovery, development and commercialization of which are the sole and exclusive responsibility of SPL.

ARTICLE IV

LICENSES AND EXCLUSIVITY

4.1 License to SPL .

4.1.1 License to Pharmacopeia Technology . Subject to the terms of Section 4.4.1, Pharmacopeia agrees to grant, and hereby grants to SPL an exclusive license under the Pharmacopeia Technology (exclusive even as to Pharmacopeia and its Affiliates) in the Territory, to make, have made, use, sell, offer to sell, import and export Agreement Products containing a Lead Compound which is a Hit or a corresponding Derivative Compound as an active ingredient. It is understood that such licenses shall include the right to conduct drug research and development, and the exclusive right to discover, develop, make, have made and use such Lead Compounds and corresponding Derivative Compounds, during the term of this Agreement.

4.1.2 License to Collaboration Technology . Pharmacopeia agrees to grant, and hereby grants to SPL an exclusive license under Pharmacopeia’s interest in the Collaboration Technology (exclusive even as to Pharmacopeia and its Affiliates), to make, have made, use, sell, offer to sell, import and export Agreement Products in the Territory. It is understood that such licenses shall include the right to conduct drug research and development, and the exclusive right to discover, develop, make, have made and use Agreement Compounds, during the term of this Agreement.

4.1.3 License to Collaboration Target-Specific Technology . Pharmacopeia agrees to grant, and hereby grants, to SPL an exclusive license (exclusive even as to Pharmacopeia and its Affiliates), under all of Pharmacopeia s interest in the Collaboration Target-Specific Technology for any and all purposes in the Territory, including the right to grant sublicenses.

4.1.4 *

4.2 Sublicenses . SPL shall have the right to sublicense the rights granted in Section 4.1 above. Each such sublicense shall be consistent with all the terms and conditions of this Agreement. SPL shall remain responsible to Pharmacopeia for all of each such Sublicensee’s applicable financial and other obligations due under this Agreement. Such Sublicensee shall not have the right to grant further sublicenses, and such sublicenses may not be assigned or transferred to any Third Party without the prior written consent of Pharmacopeia. Each sublicense shall provide for its continuation following early termination of the license rights of SPL hereunder and its assignment to Pharmacopeia. Promptly following the execution of each sublicense requiring Pharmacopeia’s consent hereunder, SPL shall give Pharmacopeia written notice of the existence and identity of each Sublicensee and identify the Agreement Product(s) sublicensed to such Sublicensee.

4.3 Direct Affiliate Licenses . Whenever SPL shall reasonably demonstrate to Pharmacopeia that, in order to facilitate direct royalty payments by an Affiliate, it is desirable that a separate license agreement be entered into between Pharmacopeia and such Affiliate, Pharmacopeia will grant such licenses directly to such Affiliate by means of an agreement which shall be consistent with all of the provisions hereof and SPL shall guarantee the Affiliate’s obligations thereunder and otherwise provide to Pharmacopeia assurances of performance satisfactory to Pharmacopeia. SPL shall reimburse Pharmacopeia for its reasonable attorneys’ fees and costs incurred in connection with any such separate license agreement.

 

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4.4 Third Party Rights .

4.4.1 Pharmacopeia Third Party Activities . It is understood that as of the Effective Date Pharmacopeia may have already granted, or on or after the Effective Date may grant, to Third Parties rights to acquire licenses for Pharmacopeia Compounds similar to SPL’s rights under this Article IV. Notwithstanding the licenses granted to SPL under Sections 4.1.1 and 4.1.4 above, it is possible that a Third Party already has or may acquire rights from Pharmacopeia with respect to one or more compounds of which Pharmacopeia is a sole or joint owner, which compounds were made and designed independently of Pharmacopeia’s activities in the Collaboration; accordingly, Pharmacopeia’s grant of rights under Sections 4.1.1 and 4.1.4 are limited to the extent that (i) a Third Party (either alone or jointly with Pharmacopeia) has filed a patent application with respect to such a compound prior to the filing by SPL (either alone or jointly with Pharmacopeia) of a patent application with respect to such a compound, or (ii) Pharmacopeia has previously granted a Third Party a license, an option to acquire a license, a right of first negotiation, field exclusivity, or a non-competition covenant with respect to such a compound, and are subject to any such grant of rights to a Third Party.

4.4.2 No Liability . It is understood and agreed that, even if Pharmacopeia complies with its obligations under this Agreement, compounds provided to Third Parties in the course of Pharmacopeia’s other business activities may result in Third Party patent applications and patents, including patent applications and patents owned by such Third Parties, or owned jointly by Pharmacopeia and such Third Parties, which could conflict with patent applications and patents owned by SPL, or jointly owned by SPL and Pharmacopeia hereunder. Pharmacopeia shall use reasonable efforts to avoid such conflict, which efforts shall be comparable to those used by Pharmacopeia in performing similar obligations under its agreements with Third Parties. It is understood that, unless SPL is damaged as a proximate result of a material breach by Pharmacopeia of any of the representations and warranties in Article VIII, then Pharmacopeia shall have no liability under this Agreement with respect to any such conflict.

4.4.3 Pharmacopeia Reports to SPL On Third Party Rights . During the period from the Effective Date until the First Commercial Sale of an Agreement Product, within thirty (30) days of a written demand by SPL concerning a Pharmacopeia license to a Third Party of a patent application owned or co-owned by Pharmacopeia, Pharmacopeia shall, to the extent it may do so without breaching any contractual or other legal obligation, provide SPL with a statement explaining why the invention(s) claimed in the patent application or technology licensed to such Third Party is independent of Pharmacopeia’s activities in the Collaboration. Such statement shall be supported by written records kept in the ordinary course of business consistent with pharmaceutical industry standards, provided that such records need not be provided to SPL at the time of providing such statement, but may have to be provided pursuant to Section 11.3. Such information shall be deemed Confidential Information of Pharmacopeia pursuant to this Agreement.

4.5 Collaboration Research Activities . SPL agrees to grant, and hereby grants, to Pharmacopeia a royalty-free, non-exclusive license under (i) SPL’s interest in the Collaboration Technology, and (ii) any Schering Technology which SPL, in its sole discretion, reasonably determines is necessary or useful for Pharmacopeia’s performance of the Collaboration, in each case to use during the term of the Collaboration and solely in performance of the Collaboration. Pharmacopeia will not be required to pay any fees to use such intellectual property, but will as a condition precedent to such use execute any consents or sublicenses required by any SPL licensor. Pharmacopeia shall not be required to execute any unreasonable consents or licenses and will not be in breach of this Agreement for failure to do so.

4.6 *

4.7 No Other Products . Neither SPL nor its Affiliates or Sublicensees shall commercialize any Hit, Lead Compound which is a Hit, Derivative Compound, Schering Derivative or other composition of matter claimed in a Collaboration Patent Right, other than as an Agreement Product in accordance with this Agreement.

ARTICLE V

PAYMENTS

5.1 Payments By Schering . In partial consideration for Pharmacopeia’s conducting research activities in the Collaboration and the rights and licenses granted to SPL herein, SPL agrees to pay to Pharmacopeia the amounts set forth in Sections 5.2, 5.3, 5.4 and 5.5. *

 

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5.2 Collaboration Funding .

5.2.1 Funding During Year One . SPL shall pay to Pharmacopeia research funding for the Collaboration at a rate of * per FTE per year during the first year of the Collaboration based upon the actual number of Pharmacopeia FTEs assigned to the Collaboration as set forth in Section 2.5.1, plus any additional FTEs (if any) agreed upon by the Parties under Section 2.3(i).

5.2.2 Funding During Subsequent Years . SPL shall pay to Pharmacopeia research funding for the Collaboration at an adjusted rate per FTE during the second year and each subsequent year of the Collaboration, based upon the actual number of Pharmacopeia FTEs assigned to the Collaboration in such year in accordance with Sections 2.5.2, 2.5.3 or 2.5.4 (as applicable), plus any additional FTEs (if any) agreed upon by the Parties under Section 2.3(i). The adjusted rate to be applied in each such year shall be* Notwithstanding the foregoing, in the event that the adjusted rate for FTE funding determined based upon*

5.2.3 Manner of Payment . As noted in Section 5.1, with respect to each Pharmacopeia FTE, *Research funding for the Collaboration under this Section 5.2 shall be payable quarterly in advance on the first day of each calendar quarter. Pharmacopeia shall send an invoice therefor to SPL fifteen (15) business days prior to the end of the preceding quarter, and SPL shall pay such invoiced amounts. It is understood that in the case of the first calendar quarter of the first year of the Collaboration, Pharmacopeia shall send an invoice to SPL as soon as practicable after the Effective Date. Each invoice will indicate the number of Pharmacopeia FTEs to be assigned to the Collaboration for such quarter and any adjustment from the prior quarter as determined in accordance with Section 5.2.4. SPL will use commercially reasonable efforts during each calendar year during the term of the Collaboration to pay its first calendar quarter Collaboration funding payments to Pharmacopeia on or before the first (1st) day of January; provided , however , that in the event SPL is unable to complete such payment, payment by SPL on or before the seventh (7th) day of January in such calendar year shall not constitute a breach or default by SPL.

5.2.4 Quarterly Adjustment . At the conclusion of each quarter, Pharmacopeia will calculate the actual number of FTEs provided by Pharmacopeia during that quarter and calculate any difference between the actual number of FTEs provided by Pharmacopeia and the number prepaid by SPL. Any overpayment or underpayment shall be reflected as a credit or additional charge, as the case may be, in the next quarterly invoice as per Section 5.2.3, and in the event that no further quarterly payments are due under this Section 5.2, then (i) any underpayment shall be paid by SPL to Pharmacopeia within fifteen (15) business days of receiving notice and invoice therefor, or (ii) Pharmacopeia shall within thirty (30) days reimburse SPL for any overpayment. For purposes of clarity and avoidance of doubt, the Parties acknowledge and agree that nothing in this Section 5.2.4 shall be construed as obligating SPL to pay for any Pharmacopeia FTEs actually working in the Collaboration during a given year of the Collaboration in excess of the number of FTEs specifically provided for in Section 2.2 during such year, unless such increased FTE support is agreed to in advance in writing by SPL.

5.3 Lead Compound Milestone . SPL shall pay to Pharmacopeia a milestone payment of *for each new Optimization Program initiated or agreed to by SPL with respect to a Screening Target based upon one or more Lead Compound(s) accepted by SPL in accordance with Section 2.8 that are Hits arising from Screening Programs conducted by Pharmacopeia. No such milestone shall be payable with respect to any Optimization Programs initiated or agreed to based upon Lead Compounds which are Schering Compounds. Such milestone payment shall be due within thirty (30) days after SPL notifies Pharmacopeia pursuant to Section 2.8.3 that it has accepted one or more Pharmacopeia Compounds as Lead Compounds. The milestone payment under this Section 5.3 shall only be payable *Further, it is understood and agreed that all amounts payable under this Section 5.3 are in addition to any milestone payments that may be due to Pharmacopeia under the corresponding provisions of the US Agreement. For the avoidance of doubt, it is understood and agreed that, for each new Optimization Program conducted by Pharmacopeia, Pharmacopeia shall be entitled to receive the milestone payment under this Section 5.3 and the milestone payment from Schering Corporation under the corresponding provision of the US Agreement.

 

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5.4 Milestone Payments .

5.4.1 Events and Amounts .

(a) Milestones for Optimization Programs based upon Schering Compounds . SPL agrees to pay to Pharmacopeia the following amounts upon attainment, by or on behalf of SPL, its Affiliates or Sublicensees, of the indicated milestones with respect to any new Agreement Compounds/Agreement Products discovered by Pharmacopeia in performance of an Optimization Program based upon one or more Lead Compounds which are Schering Compounds (i.e., any Derivative Compounds resulting from such Optimization Program and/or any Schering Derivatives derived from such Derivative Compounds):

 

  (i) *upon nomination of a Development Candidate;

 

  (ii) *upon the filing and Acceptance of an IND or its equivalent;

 

  (iii) *upon initiation of treatment of the first patient in a Phase III clinical study;

 

  (iv) *upon filing and Acceptance of an HRD with the applicable regulatory authority in a Major Market; and

 

  (v) *upon Regulatory Approval in a Major Market.

(b) Milestones for Optimization Programs based upon Hits . SPL agrees to pay to Pharmacopeia the following amounts upon attainment, by or on behalf of SPL, its Affiliates or Sublicensees, of the indicated milestones with respect to an Agreement Compound/Agreement Product arising from an Optimization Program based upon one or more Lead Compounds which are Hits, (i.e., any such Lead Compounds, related Hits, Derivative Compounds resulting from such Optimization Program and/or Schering Derivatives derived from such Lead Compounds, Hits or Derivative Compounds):

 

  (i) *upon nomination of a Development Candidate;

 

  (ii) *upon the filing and Acceptance of an IND or its equivalent;

 

  (iii) *upon initiation of treatment of the first patient in a Phase III clinical study;

 

  (iv) *upon filing and Acceptance of an HRD with the applicable regulatory authority in a Major Market; and

 

  (v) *upon Regulatory Approval in a Major Market.

It is understood and agreed that all amounts payable under this Section 5.3.1 are in addition to any milestone payments that may be due to Pharmacopeia under the terms of the US Agreement.

5.4.2 Development Candidate . A Development Candidate shall have been deemed to have been nominated upon the earlier of the date (i) the Schering-Plough Research Institute Project Assessment Committee or its successor approves proceeding with full development of such compound, or (ii) SPL (or its Affiliate) initiates in vivo toxicology trials necessary, and meeting U.S. FDA (or corresponding European or Japanese) standards, for obtaining approval for use of such Agreement Compound in human clinical trials. Within thirty (30) days after the nomination of a Development Candidate, SPL shall notify Pharmacopeia thereof.

5.4.3 Manner of Payment . All payments made to Pharmacopeia by SPL pursuant to Section 5.4.1(a) or (b) shall be due within thirty (30) days after the achievement of the corresponding milestone and shall be nonrefundable and not creditable against other amounts due to Pharmacopeia. The payments provided for under this Section 5.4 shall only be payable once upon the first achievement of the indicated milestone with respect to an Agreement Compound and/or Agreement Product developed against a particular Target and no additional payments shall be due on subsequent or repeated achievement of the same milestone for another Agreement Compound and/or Agreement Product developed against the same Target. No milestones shall be payable under this Section 5.4 with respect to any compounds or products other than Agreement Compounds and Agreement Products, nor shall any payments be due under this Section 5.4 with respect to any Agreement Products discovered by SPL with respect to Targets which are not the subject of a Screening Program and/or Optimization Program, as provided in Section 2.11.

 

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5.5 Royalties . In partial consideration for the know-how licenses, patent licenses and other rights granted to SPL hereunder, SPL shall pay royalties to Pharmacopeia based upon the sales of Agreement Products in the Territory. The parties acknowledge and agree that, except as expressly set forth herein, SPL’s obligation to pay such royalties is not conditioned upon the existence of patent protection for the Agreement Products.

5.5.1 Base Royalty . SPL shall pay to Pharmacopeia running royalties on Net Sales of Agreement Products by SPL, its Affiliates and Sublicensees in the Territory, as follows:

 

  (i) *of Net Sales of Agreement Products where the Agreement Compound in such Agreement Product is (1) a Lead Compound which is a Hit, or (2) a Derivative Compound discovered by Pharmacopeia in an Optimization Program based upon a Lead Compound which is a Hit, or (3) a corresponding Schering Derivative; or

 

  (ii) * of Net Sales of Agreement Products where the Agreement Compound in such Agreement Product is a Derivative Compound discovered by Pharmacopeia in an Optimization Program based upon a Lead Compound which is a Schering Compound;

 

  (iii) *of Net Sales of Agreement Products where the Agreement Compound in such Agreement Product is (1) a Lead Compound which is a Hit, or (2) a Derivative Compound, and in each case where such Agreement Product was developed and commercialized by SPL as a result of an independent screening program conducted by SPL pursuant to Section 2.11 against a Target which was not the subject of a Screening Program or Optimization Program under this Agreement; or

 

  (iv) *of net sales (to be determined in the same manner as Net Sales) of a pharmaceutical product containing as an active ingredient a Schering Derivative derived from a Derivative Compound discovered by Pharmacopeia in an Optimization Program based upon a Lead Compound which is a Schering Compound.

5.5.2 Royalty Term for Agreement Products . SPL’s obligation to pay royalties to Pharmacopeia under Sections 5.5.1(i), 5.5.1(ii), 5.5.1(iii) or 5.5.1(iv), as applicable, shall continue for each Agreement Product, on a country-by country basis, until the date which is the later of *

5.5.3 Single Royalty; Non-Royalty Sales . No royalty shall be payable under Section 5.5.1 above with respect to sales of Agreement Products among SPL, its Affiliates and Sublicensees for resale; however, a royalty shall be payable upon such resale by SPL’s Affiliates and Sublicensees to any Third Party. In no event shall more than one royalty be due hereunder with respect to any Agreement Product unit even if covered by more than one patent included in the Pharmacopeia Technology or Collaboration Technology. For purposes of clarity and avoidance of doubt, the Parties acknowledge and agree that under no circumstances will any royalty ever be payable under Sections 5.5.1(i) or 5.5.1(ii) with respect to sales of any Agreement Product resulting from an independent screening programs conducted by SPL pursuant to Section 2.11. No royalties shall accrue on the disposition of any Agreement Product in reasonable quantities by SPL, its Affiliates or its Sublicenses as (i) samples (promotional or otherwise), (ii) donations (for example, to non-profit institutions or government agencies for a non-commercial purpose), (iii) for use in clinical studies, or (iv) free of charge in compassionate use and/or indigent care programs.

5.5.4 Third Party Royalties .

(a) SPL Responsibilities . SPL shall be responsible for the payment of any royalties due to licenses obtained from Third Parties relating to the manufacture, use, marketing, sale or distribution of Agreement Products by SPL, its Affiliates or Sublicensees under the Collaboration Technology or Schering Technology.

 

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(b) Third Party Royalty Offset . Notwithstanding Section 5.5.4(a) above, if a Third Party alleges that the manufacture, use or sale of an Agreement Product infringes its patents, based solely on the practice of the Pharmacopeia Technology, Pharmacopeia and SPL shall consult regarding whether a license should be taken from such Third Party. If Pharmacopeia and SPL agree that such a license is required, SPL, its Affiliates or Sublicensees may, with respect to sales of such Agreement Product, pay royalties directly (or indirectly through Pharmacopeia) to the Third Party whose patents may be infringed by such sales. SPL may reduce any royalty due Pharmacopeia under Section 5.5.1 to reimburse SPL for any such royalties actually paid to Third Parties; provided that the amount of the reduction shall be equal to * of the royalty actually paid to such Third Parties with respect to sales of the Agreement Product in such country; provided , however , that in no event shall the royalty due Pharmacopeia for any calendar quarter, with respect to any such Agreement Product, be thereby reduced to * of the royalty due Pharmacopeia under Section 5.5.1 with respect to Net Sales in such country. If the Parties cannot promptly reach agreement they shall appoint an independent patent counsel reasonably acceptable to each of them to give an opinion, which will be binding as between the Parties, and the parties shall have no further recourse to dispute such opinion (including, without limitation, the provisions of Section 11.3, which shall not apply). If it is the independent patent counsel’s opinion that the patent is valid and infringed by the sale of such Agreement Product due to use of the Pharmacopeia Technology, SPL may settle the matter in its sole discretion on such terms as it deems appropriate, provided that such settlement does not contain an admission or acknowledgment of infringement or invalidity.

5.5.5 Compulsory Royalty Reductions . If the royalties set forth herein are higher than the maximum royalties permitted by the law or regulation in any country or territory or possession thereof in the world, the royalty payable for sales in such country, territory or possession shall be equal to the maximum permitted royalty under such law or regulations.

5.5.6 Royalty Overpayment . In the event SPL pays Pharmacopeia royalties in excess of the amounts due under Section 5.5.1 herein, SPL shall promptly notify Pharmacopeia providing a written explanation of the amount of overpayment. Any such overpayment shall be fully creditable against royalties subsequently due hereunder.

5.6 Reports; Payment of Royalty; Payment Exchange Rate and Currency Conversions .

5.6.1 Royalty Reports and Payments . After the First Commercial Sale of an Agreement Product on which royalties are payable by SPL, its Affiliate or Sublicensees hereunder, SPL shall make quarterly written reports to Pharmacopeia within sixty (60) days after the end of each calendar quarter, stating in each such report separately for SPL and each of its Affiliates and Sublicensees the number, description, and aggregate Net Sales by country of each Agreement Product sold during the calendar quarter upon which a royalty is payable under Section 5.5 above. Subject to any reductions permitted pursuant to the express terms of this Agreement, concurrently with the making of such reports, SPL shall pay to Pharmacopeia royalties at the rates specified in Section 5.5.1.

5.6.2 Payment Method . All payments due under this Agreement shall be made by bank wire transfer in immediately available funds to an account designated by Pharmacopeia. All payments hereunder shall be made in U.S. dollars. Any payments that are not paid on the date such payments are due under this Agreement shall bear interest, calculated on the number of days such payment is delinquent, at the lesser of: (i) the prime rate as reported by the Chase Manhattan Bank, New York, New York, on the date such payment is due, plus an additional two percent (2%), or (ii) the maximum rate permitted by applicable law.

5.6.3 Place of Royalty Payment and Currency Conversions . Royalties shall be deemed payable by the entity making the Net Sales from the country in which earned in local currency and subject to foreign exchange regulations then prevailing. Royalty payments shall be made in United States dollars to the extent that free conversion to United States dollars is permitted. The rate of exchange to be used in any such conversion from the currency in the country where such Net Sales occurs shall be in accordance with the policy set forth in Exhibit A hereto. If, due to restrictions or prohibitions imposed by national or international authority, payments cannot be made as aforesaid, the Parties shall consult with a view to finding a prompt and acceptable solution, and SPL or its designated Affiliates will, from time to time, deal with such monies as Pharmacopeia may lawfully direct at no additional

 

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out-of-pocket expense to SPL. Notwithstanding the foregoing, if royalties in any country cannot be remitted to Pharmacopeia for any reason within six (6) months after the end of the calendar quarter during which they are earned, then SPL shall be obligated to deposit the royalties in a bank account in such country in the name of Pharmacopeia.

5.7 Maintenance of Records; Audits .

5.7.1 Records; Inspection . SPL and its Affiliates shall keep complete, true and accurate books of account and records for the purpose of determining the royalty amounts payable under this Agreement, which books and records shall be maintained in accordance with SPL’s records retention policies. Upon prior written notice from Pharmacopeia, SPL shall, within a period not to exceed forty-five (45) days, permit an independent certified public accounting firm of nationally recognized standing selected by Pharmacopeia and reasonably acceptable to SPL, at Pharmacopeia’s expense, to have access during normal business hours to examine pertinent books and records of SPL and/or its Affiliates as may be reasonably necessary to verify the accuracy of the royalty reports hereunder. The examination shall be limited to pertinent books and records for any calendar year ending not more than thirty-six (36) months prior to the date of such request. Such inspections may be made no more than once each calendar year. In the event that the accounting firm correctly concludes that a variation or error has occurred resulting in an underpayment of royalties by SPL of five percent (5)% or more of the amount actually due for the period covered by the inspection, SPL shall pay to Pharmacopeia such additional amounts, as well as the costs relating to the inspection, within thirty (30) days of receipt of an invoice for such amounts. Any overpayment of royalties by SPL discovered through such audit shall be fully creditable against royalties subsequently due hereunder. SPL may designate competitively sensitive information which such auditor may not disclose to Pharmacopeia; provided , however , that such designation shall not encompass the auditor’s conclusions. The accounting firm shall disclose to Pharmacopeia only whether the royalty reports are correct or incorrect and the specific details concerning any discrepancies. No other information shall be provided to Pharmacopeia. The accounting firm employees shall sign confidentiality agreements acceptable to SPL as a condition precedent to their inspection. SPL shall include in each sublicense granted by it pursuant to this Agreement a provision requiring the Sublicensee to make reports to SPL, to keep and maintain records of sales made pursuant to such sublicense and to grant access to such records by Pharmacopeia’s independent accountant to the same extent required of SPL under this Agreement. Upon expiration of the thirty-six (36) month period immediately following the receipt by Pharmacopeia of SPL’s fourth quarter royalty report for a given calendar year in accordance with Section 5.6.1, the calculation of royalties payable with respect to such year shall be binding and conclusive upon Pharmacopeia, and SPL, its Affiliates and its Sublicensees shall be released from any liability or accountability with respect to royalties for such year, except for instances of fraud or other intentional misconduct by SPL.

5.8 Coordination With Payments under US Agreement . The milestones and royalties payable by SPL under Sections 5.3, 5.4 and 5.5 are in consideration for the rights and licenses granted to SPL under this Agreement and are in addition to any amounts payable to Pharmacopeia under the US Agreement. It is understood and agreed that, with respect to the specific milestones payable under Sections 5.4.1(a)(i)-(iii) and 5.4.1(b)(i)-(iii), the occurrence of the same milestone event will result in milestone payment obligations under both this Agreement and the corresponding provisions of the US Agreement. However, the specific milestones payable under Sections 5.4.1(a)(iv) and (v) and Sections 5.4.1(b)(iv) and (v) under this Agreement and the analogous milestones under the US Agreement shall be paid, respectively, upon occurrence of the relevant milestone event specified in this Agreement or the US Agreement.

5.9 Tax Matters .

5.9.1 Withholding Taxes . All royalty amounts required to be paid to Pharmacopeia pursuant to this Agreement shall be paid with deduction for withholding for or on account of any taxes (other than taxes imposed on or measured by net income) or similar governmental charge imposed by a jurisdiction other than the United States (“Withholding Taxes”) to the extent Pharmacopeia and/or its Affiliates or their successors has the lawful rights to utilize the Withholding Taxes paid by SPL as a credit against Pharmacopeia’s and/or its Affiliates regular U.S. tax liability. SPL shall provide Pharmacopeia documentation evidencing payment of any Withholding Taxes hereunder in a manner that is satisfactory for purposes of the U.S. Internal Revenue Service. Any Withholding Taxes paid when due hereunder shall be for the account of Pharmacopeia and shall not be included in the calculation of Net Sales. Payments of Withholding Taxes made by SPL pursuant to this Section 5.9.1 shall be made based upon financial

 

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information provided to SPL by Pharmacopeia, and to the extent that such information is incorrect Pharmacopeia shall be liable for any deficiency, and any fine, assessment or penalty imposed by any taxing authority in the Territory for any deficiency in the amount of any such Withholding Taxes, or the failure to make payment of Withholding Taxes, based upon such incorrect information. If SPL is required to pay any such deficiency, or any fine, assessment or penalty for any such deficiency based upon such incorrect information (except to the extent caused by SPL’s gross negligence or willful misconduct), Pharmacopeia shall promptly reimburse SPL for such payments, which shall not be included in the calculation of Net Sales.

5.10 Product Development Costs . SPL shall, at SPL’s expense, be responsible for conducting all development of Agreement Compounds, Agreement Products, Schering Compounds, and all commercialization of Agreement Products.

ARTICLE VI

PATENTS AND INVENTIONS

6.1 Ownership of Schering Technology and Pharmacopeia Technology . It is understood and agreed that (i) SPL shall own all Schering Technology including, without limitation, Schering Improvements, and (ii) Pharmacopeia shall own all Pharmacopeia Technology including, without limitation, Pharmacopeia Improvements.

6.2 Ownership of Collaboration Technology . The Parties anticipate that the Collaboration may result in new inventions, discoveries and innovations, as well as improvements to existing technologies, whether patentable or not, within the Collaboration Technology. Ownership of Collaboration Technology shall be determined based upon U.S. Patent Laws and the following guidelines; provided , however , that ownership rights to all Collaboration Technology shall be subject to the applicable licenses and other rights granted under Article IV of this Agreement.

(a) Inventions by SPL Employees . Title to all Collaboration Technology invented solely by employees of SPL working on the Collaboration at Pharmacopeia, together with any Derivative Compounds synthesized by Pharmacopeia pursuant to Section 2.9, shall be deemed to be owned by SPL.

(b) Inventions by Pharmacopeia Employees . Title to all Collaboration Technology invented solely by employees of Pharmacopeia shall be deemed to be owned by Pharmacopeia.

(c) Joint Inventions . Title to all Collaboration Technology invented jointly by one or more employees of SPL working on the Collaboration at Pharmacopeia, and one or more employees of Pharmacopeia shall be deemed to be jointly owned by SPL and Pharmacopeia.

6.3 Filing, Prosecution and Maintenance of Patents .

6.3.1 Collaboration Technology . SPL shall have the right to prepare, file, prosecute and maintain in such countries as it deems appropriate in its discretion, at its own expense and upon appropriate consultation with Pharmacopeia, patent applications and patents, and to conduct any interferences, re-examinations, reissues, oppositions or requests for patent term extension or governmental equivalents thereto within the Collaboration Technology, and Pharmacopeia shall give reasonable cooperation in connection therewith, at SPL’s request and expense. SPL shall provide Pharmacopeia with copies of any new patent applications claiming Collaboration Technology which are proposed to be filed by SPL, as provided in Section 6.4.1. In the event that SPL does not file a patent or patent application claiming an invention within such Collaboration Technology, or if it ceases to so prosecute, maintain, conduct any interferences, re-examinations, reissues, oppositions or requests for patent term extension or governmental equivalents thereto relating to such an invention, Pharmacopeia shall have the right, in its sole discretion, to undertake such activities at its own expense, and SPL shall give reasonable cooperation in connection therewith, at Pharmacopeia’s expense.

6.3.2 Schering Technology . SPL shall have the right to prepare, file, prosecute and maintain in such countries as it deems appropriate in its discretion, at its own expense, patent applications and patents, and to conduct any interferences, re-examinations, reissues, oppositions or requests for patent term extension or governmental equivalents thereto within the Schering Technology and Pharmacopeia shall give reasonable cooperation in connection therewith, at SPL’s request and expense.

 

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6.3.3 Pharmacopeia Technology . Pharmacopeia shall have the right to prepare, file, prosecute and maintain in such countries as it deems appropriate in its discretion, at its own expense, patent applications and patents, and to conduct any interferences, re-examinations, reissues, oppositions or requests for patent term extension or governmental equivalents thereto within the Pharmacopeia Technology, and SPL shall give reasonable cooperation in connection therewith, at Pharmacopeia’s request and expense.

6.4 Cooperation .

6.4.1 Cooperation . Upon request, and at the requesting Party ’s expense, each of Pharmacopeia and SPL shall provide the other Party reasonable assistance to prepare, file, prosecute and maintain patents and patent applications covering any Collaboration Technology, Schering Improvements or Pharmacopeia Improvements which the requesting Party has the right to file. Reasonable assistance shall include, without limitation, providing the requesting Party with necessary or useful data and information relating to the Collaboration Technology, Schering Improvements or Pharmacopeia Improvements, as the case may be, and reasonable access to the inventors of said inventions, as well as causing the execution of required patent assignments and/or other documents. With respect to all patent applications claiming Collaboration Technology, or any Derivative Compounds, Lead Compounds which are Hits, or Schering Derivatives, the filing Party shall give the non-filing Party an opportunity to review the text of such patent applications before filing, shall consult with the non-filing Party with respect thereto, and shall supply the non-filing Party with a copy of the applications as filed, together with notice of its filing date and serial number. SPL will identify to Pharmacopeia any of SPL’s proprietary information contained in such documents to be provided to Pharmacopeia to ensure that Pharmacopeia will protect SPL’s proprietary information, including without limitation, information relating to Targets. In addition, with respect to applications which do not include Pharmacopeia inventors, SPL may redact or provide in coded form any information contained in such documents to be provided to Pharmacopeia to the extent necessary (in SPL’s opinion) to protect SPL’s proprietary information, including without limitation, information relating to Targets. Pharmacopeia and SPL shall each keep the other Party advised of the status of the actual and prospective patents and patent applications within the Collaboration Patent Rights for which it is responsible, and upon the written request of the other Party, will provide advance copies of any substantive papers related to the filing, prosecution and maintenance of such Collaboration Patent Rights.

6.5 Enforcement .

6.5.1 Notice . Each Party shall promptly notify the other of its knowledge of any actual or potential infringement of the Collaboration Technology by a Third Party.

6.5.2 Collaboration Technology . SPL shall have the initial right, but not the obligation, to take reasonable legal action to enforce against infringements by Third Parties or defend any declaratory judgment action relating to any patent within the Collaboration Technology at its sole cost and expense. If, within six (6) months following receipt of notice of such infringement from Pharmacopeia (or written notice of a declaratory judgment action alleging invalidity or unenforceability of such Collaboration Technology), SPL does not take such action against a commercially significant infringement, Pharmacopeia shall, in its sole discretion, have the right, but not the obligation to take such action at its sole expense.

6.5.3 Schering Technology and Pharmacopeia Technology . It is understood and agreed that Pharmacopeia shall have the sole right, but not the obligation, to initiate and conduct legal proceedings to enforce the Pharmacopeia Technology against any actual or threatened infringement or misappropriation or defend any declaratory judgment action relating thereto, at its sole expense, and that SPL shall have the sole right, but not the obligation, to initiate and conduct legal proceedings to enforce the Schering Technology against any actual or threatened infringement or misappropriation or defend any declaratory judgment action relating thereto, at its sole expense.

6.5.4 Cooperation; Costs and Recoveries . Each Party agrees to render such reasonable assistance as the enforcing Party may request, and at the enforcing Party’s expense. Costs of maintaining any such action shall be paid by the Party bringing the action

 

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and any damages or settlements recovered therefrom shall belong to such Party. To the extent that SPL recovers any lost profits or other recovery based upon Third Party sales of infringing products, Pharmacopeia shall receive an equitable share of such recovery, as determined based upon the royalties Pharmacopeia would have been entitled to under this Agreement on Net Sales by SPL, its Affiliates or Sublicensees of the relevant Agreement Products corresponding to such lost profits. If SPL, in its sole discretion, agrees to settle any such infringement action by granting a sublicense to the Third Party infringer, and such Third Party, but for the grant of such sublicense, would be infringing a claim of an issued patent in the Collaboration Technology, or a composition-of-matter claim of an issued patent in the Schering Technology, SPL shall be entitled to receive all consideration payable by such Third Party for the grant of the license; provided , however , that net sales of such Third Party products in the Territory on which SPL receives such consideration (including, without limitation, running royalties or lump sum payments) shall be treated as Net Sales for purposes of this Agreement, and further provided that, notwithstanding anything herein to the contrary, SPL’s royalty obligations to Pharmacopeia with respect to such Third Party sales in any calendar quarter shall not exceed fifty percent (50%) of the royalties received by SPL from such Third Party for the same quarter.

6.6 Infringement Claims . If the manufacture, sale or use of any Agreement Product pursuant to this Agreement because of the practice of the Pharmacopeia Technology, Collaboration Technology or Schering Technology, results in any claim, suit or proceeding alleging patent infringement against Pharmacopeia or SPL (or their respective Affiliates or Sublicensees), such Party shall promptly notify the other Party hereto in writing setting forth the facts of such claim in reasonable detail. The Party subject to such claim shall have the exclusive right and obligation to defend and control the defense of any such claim, suit or proceeding, at its own expense, using counsel of its own choice; provided , however , it shall not enter into any settlement which admits or concedes that any aspect of (i) the Schering Technology or Collaboration Technology in the case of Pharmacopeia, and (ii) the Pharmacopeia Technology or Collaboration Technology in the case of SPL, is invalid or unenforceable without the prior written consent of such other Party. The Party subject to the claim shall keep the other Party hereto reasonably informed of all material developments in connection with any such claim, suit or proceeding.

6.7 Certification under Drug Price Competition and Patent Restoration Act . Pharmacopeia and SPL each shall immediately give written notice to the other of any certification of which they become aware filed pursuant to 21 U.S.C.§§355(b)(2)(A)(iv) and 355(j)(2)(A)(vii) claiming that Collaboration Patent Rights do not cover the use or sale of any product(s) equivalent to an existing Agreement Product(s) by a Third Party. SPL shall have the right to bring an infringement action, in its sole discretion and at its own expense, in its own name and/or in the name of Pharmacopeia, subject to Section 6.5 above. The provisions of Section 6.5.4 shall apply to any such infringement action.

6.8 Patent Term Restoration . The Parties hereto shall give reasonable cooperation to each other in obtaining patent term restoration or supplemental protection certificates or their equivalents in any country in the Territory where applicable to the Collaboration Technology.

ARTICLE VII

CONFIDENTIALITY

7.1 Confidential Information . Except as expressly provided herein, the Parties agree that, *, the receiving Party shall not disclose and except as expressly provided in this Article 7, shall not use for any purpose any confidential information (“Confidential Information”) furnished to it by the disclosing Party hereto pursuant to this Agreement except to the extent that it can be established by the receiving Party by competent proof that such information:

(i) was already known to the receiving Party, other than under an obligation of confidentiality, at the time of disclosure;

(ii) was generally available to the public or otherwise part of the public domain at the time of its disclosure to the receiving Party;

(iii) became generally available to the public or otherwise part of the public domain after its disclosure and other than through any act or omission of the receiving Party in breach of this Agreement;

 

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(iv) was independently developed by the receiving Party as demonstrated by documented evidence prepared contemporaneously with such independent development; or

(v) was subsequently lawfully disclosed to the receiving Party, other than under a duty of confidentiality, by a Third Party that had the right to make such disclosure.

7.2 Permitted Use and Disclosures . Each Party hereto may use or disclose Confidential Information disclosed to it by the other Party to the extent such information is included in the Pharmacopeia Technology, Schering Technology or Collaboration Technology, as the case may be, and to the extent (i) such use or disclosure is reasonably necessary and permitted in the exercise of the rights granted hereunder in filing or prosecuting patent applications, prosecuting or defending litigation, (ii) such disclosure is reasonably required to be made to any institutional review board of any entity conducting clinical trials with Agreement Compound(s) and/or Agreement Product(s), or to any governmental or other regulatory agency, in order to gain approval to conduct clinical trials or to market Agreement Compound(s) and/or Agreement Products, (iii) such disclosure is required by law, regulation, rule, act or order of any governmental authority, court, or agency, or is made in connection with submitting required information to tax or other governmental authorities, or (iv) such disclosure or use is reasonably required in conducting clinical trials, or making a permitted sublicense or otherwise exercising license rights expressly granted to it by the other Party pursuant to the terms of this Agreement; in each case, provided that if a Party is required to make any such disclosure of another Party’s Confidential Information, other than pursuant to a confidentiality agreement, it will give reasonable advance notice to the other Party of such disclosure and, save to the extent inappropriate in the case of patent applications, will use its reasonable diligent efforts to secure confidential treatment of such Confidential Information in consultation with the other Party prior to its disclosure (whether through protective orders or otherwise) and disclose only the minimum necessary to comply with such requirements.

7.3 Return of Confidential Information . Following termination of this Agreement, at any time upon request of the disclosing Party, the receiving Party will return all documents, and copies thereof, containing the disclosing Party’ s Confidential Information that are still in the receiving Party’s possession or control; however, the receiving Party may retain one copy of such documents in a secure location solely for the purpose of determining its obligations hereunder, to comply with any applicable regulatory requirements, or to defend against any product liability claims.

7.4 Nondisclosure of Terms . Each of the Parties hereto agrees not to disclose to any Third Party the existence or the terms of this Agreement without the prior written consent of each other Party hereto, except to such Party’s attorneys, advisors, investors and others on a need to know basis under circumstances that reasonably ensure the confidentiality thereof, or to the extent required by law. Notwithstanding the foregoing, the Parties will agree upon a press release to announce the effectiveness of this Agreement, together with a corresponding Q&A outline for use in responding to inquiries about the Agreement; and in such event, Pharmacopeia and SPL may each disclose to Third Parties the information contained in such press release and Q&A without the need for further approval by the other. In addition, Pharmacopeia may make public statements regarding progress with respect to the development and commercialization of Agreement Compounds and/or Agreement Products, including announcement of the achievement of milestones, following consultation with SPL and with the written consent of SPL. Nothing in this Section 7.4 shall prohibit a Party from making such disclosures to the extent reasonably required under applicable federal or state securities laws or any rule or regulation of any nationally recognized securities exchange. In such event, however, the disclosing Party shall use good faith efforts to notify and consult with the other Party prior to such disclosure and, where applicable, shall diligently seek confidential treatment to the extent available.

7.5 Publication . Any manuscript by SPL or Pharmacopeia or their Affiliates describing Agreement Products shall be subject to the prior review of the other Party at least ninety (90) days prior to submission. Further, to avoid loss of patent rights as a result of premature public disclosure of patentable information, the receiving Party shall notify the disclosing Party in writing within thirty (30) days after receipt of a disclosure whether the receiving Party desires to file a patent application on any invention disclosed in such scientific results. In the event that the receiving Party desires to file such a patent application, the disclosing Party shall withhold publication or disclosure of such scientific results until the earlier of (i) a patent application is filed thereon, or (ii) the Parties

 

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determine after consultation that no patentable invention exists, or (iii) one hundred and eighty (180) days after receipt by the disclosing Party of the receiving Party’s written notice of the receiving Party’s desire to file such patent application, or such other period as is reasonable for seeking patent protection. Further, if such scientific results contain the information of the receiving Party that is subject to use and nondisclosure restrictions under this Article 7, the disclosing Party agrees to remove such information from the proposed publication or disclosure.

7.6 Pharmacopeia Employees . All Pharmacopeia employees assigned to work exclusively on Collaboration research projects pursuant to Section 2.5, shall be required to have read and understood the Collaboration Business Conduct Policy. Any Pharmacopeia employees assigned to work exclusively on Collaboration research projects shall also be subject to non-compete obligations, as set forth below, with respect to any Target with respect to which Collaboration research efforts directed to such Target are performed at Pharmacopeia (including, without limitation, the design and synthesis of Derivative Compounds based on Lead Compounds). None of the individual Pharmacopeia chemists participating in Target specific collaboration research shall *Pharmacopeia shall be liable for any breach of the Collaboration Business Conduct Policy and/or these non-compete obligations by its employees. * Pharmacopeia shall use reasonably diligent efforts to ensure that its employees working on the Collaboration do not disclose or provide access to any Collaboration Target-Specific Technology, Schering Technology, or the results of any screening or other Target specific research performed at Pharmacopeia in the Collaboration, to any Pharmacopeia employees not working on the Collaboration (except to the extent reasonably necessary for Pharmacopeia to ensure its compliance with its exclusivity obligations hereunder) or to any Third Parties.

ARTICLE VIII

REPRESENTATIONS, WARRANTIES AND COVENANTS

8.1 SPL . SPL warrants, represents and covenants on behalf of itself and its Affiliates that: (i) it has the legal right and power to extend the rights granted in this Agreement; (ii) it has the legal power, authority and right to enter into this Agreement, and to perform all its obligations hereunder, and (iii) it has not previously granted, and during the term of this Agreement will not knowingly make any commitment or grant any rights which in any material way conflict with the rights and licenses granted herein.

8.2 Pharmacopeia . Pharmacopeia represents, warrants and covenants on behalf of itself and its Affiliates that: (i) it has the legal right and power to extend the rights granted in this Agreement; (ii) it has the legal power, authority and right to enter into this Agreement, and to perform all its obligations hereunder; (iii) it has not previously granted, and during the term of this Agreement will not knowingly make any commitment or grant any rights which in any material way conflict with the rights and licenses granted herein; (iv) to the best of its knowledge as of the Effective Date, there are no existing or threatened actions, suits or claims pending against it with respect to the Pharmacopeia Technology; (v) to the best of its knowledge as of the Effective Date, it is not aware of any Existing Pharmacopeia Know-How which is not available for use for all purposes contemplated by this Agreement; and (vi) to the best of its knowledge as of the Effective Date, it owns or controls all of the Pharmacopeia Technology, and has the rights to grant the licenses or sublicenses granted to SPL hereunder with respect thereto.

8.3 Compliance with Agreement and Laws . Each Party shall comply in all material respects with the terms of this Agreement and with all laws, rules and regulations applicable to the discovery, development, manufacture, distribution, import and export and sale of pharmaceutical products pursuant to this Agreement.

8.4 Disclaimer . SPL and Pharmacopeia expressly disclaim any representation, warranty or guaranty that the Collaboration will be successful. EXCEPT AS OTHERWISE EXPRESSLY SET FORTH IN THIS AGREEMENT, PHARMACOPEIA AND SPL AND THEIR RESPECTIVE AFFILIATES MAKE NO REPRESENTATIONS AND EXTEND NO WARRANTIES OR CONDITIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED, WITH RESPECT TO THE PHARMACOPEIA TECHNOLOGY, THE SCHERING TECHNOLOGY, THE COLLABORATION TECHNOLOGY, LEAD COMPOUNDS, DERIVATIVE COMPOUNDS, AGREEMENT COMPOUNDS OR AGREEMENT PRODUCTS, OR INFORMATION DISCLOSED PURSUANT TO ARTICLE VII, AND EXPRESSLY DISCLAIM ALL WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, VALIDITY OF THE PHARMACOPEIA TECHNOLOGY, COLLABORATION TECHNOLOGY OR SCHERING TECHNOLOGY (IN EACH CASE, WHETHER PATENTED OR UNPATENTED), OR NONINFRINGEMENT OF THE INTELLECTUAL PROPERTY RIGHTS OF THIRD PARTIES.

 

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ARTICLE IX

INDEMNIFICATION

9.1 Indemnification by SPL . SPL shall indemnify, defend and hold harmless Pharmacopeia and its Affiliates, and each of its and their respective employees, officers, directors and agents (the “Pharmacopeia Indemnitees”) from and against any and all liability, loss, claims, damage, cost, and expense (including reasonable attorneys’ and professionals’ fees and other expenses of litigation) (collectively, a “Liability”) arising out of or in connection with Third Party claims relating to (i) the discovery, development, manufacture, use, testing, marketing, sale or other disposition of Agreement Products by or on behalf of SPL or its Affiliates or Sublicensees, (ii) performance of the Collaboration by SPL, (iii) any injury, illness or disease suffered by any SPL employees in connection with the performance of the Collaboration, (iv) the use of any and all Targets with respect to which research activities are conducted in the Collaboration, including without limitation claims in connection with materials relating to such Target, or (v) any breach by SPL of its representations and warranties made under this Agreement, except, in each case, to the extent such Liabilities result from the gross negligence or willful misconduct of Pharmacopeia, its Affiliates, or any of their respective employees, officers, directors or agents.

9.2 Indemnification by Pharmacopeia . Pharmacopeia shall indemnify, defend and hold harmless SPL and its Affiliates, and each of its and their respective employees, officers, directors and agents (the “SPL Indemnitees”) from and against any Liability (as defined above) arising out of or in connection with Third Party claims relating to (i) the performance of the Collaboration by Pharmacopeia except to the extent directly related to the use of Targets, (ii) any injury, illness or disease suffered by any Pharmacopeia employees in connection with the performance of the Collaboration, (iii) any product based upon a Pharmacopeia Compound developed, manufactured, used, sold or otherwise distributed by or on behalf of Pharmacopeia, its Affiliates or Licensees, as permitted under this Agreement (including, without limitation, product liability and patent infringement claims), (iv) any breach of Pharmacopeia’s contractual obligations to Third Parties, or (v) any breach by Pharmacopeia of its representations and warranties made under this Agreement, except, in each case, to the extent such Liabilities result from the gross negligence or willful misconduct of SPL, its Affiliates, or any of their respective employees, officers, directors or agents.

9.3 No Consequential Damages . Except with respect to Third Party claims as provided for under Sections 9.1 and 9.2, in no event shall any Party to this Agreement have any claims against or liability to the other Party for any special, consequential or incidental damages arising under this Agreement under any theory of liability.

9.4 Procedure . In the event that any Indemnitee intends to claim indemnification under this Article IX, it shall promptly notify the other Party in writing of any such alleged Liability. The indemnifying Party shall have the right to control the defense thereof with counsel of its choice; provided , however , that any Indemnitee shall have the right to retain its own counsel, with the fees and expenses to be paid by the indemnifying Party, if representation of such Indemnitee by the counsel retained by the indemnifying Party would be inappropriate due to actual or potential differing interests between such Indemnitee and any other Party represented by such counsel in such proceeding. The affected Indemnitees shall cooperate reasonably with the indemnifying Party and its legal representatives in the investigation and defense of any action, claim or liability covered by this Article IX. Neither Party may settle a claim or action related to a Liability for which it or the other Party seeks indemnification hereunder without the consent of the other Party, if such settlement would impose any monetary obligation on the other Party or require the other Party to submit to an injunction or otherwise limit the other Party’ s rights under this Agreement. Any payment made by a Party to settle any such claim or action shall be at its own cost and expense.

9.5 Insurance . Each Party shall obtain and maintain throughout the term of this Agreement statutory Workers’ Compensation and Employer’s Liability insurance covering all employees engaged in the performance of work under this Agreement. Each Party shall provide the other Party with evidence of such insurance and/or self-insurance program, upon request.

 

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ARTICLE X

TERM AND TERMINATION

10.1 Term and Expiration . This Agreement shall be effective as of the Effective Date and unless terminated earlier as provided in this Article X or by mutual written agreement of the Parties, the term of this Agreement shall continue in full force and effect, on a country-by-country and product-by-product basis, until SPL and its Affiliates and Sublicensees have no further obligation to pay royalties under Article V hereof in a country, at which time the Agreement shall expire in its entirety in such country and the Parties shall have no further payment obligations or other financial obligations to each other with respect to the continuing use in such country of Pharmacopeia Technology, Schering Technology and/or Collaboration Technology, as the case may be, in the manner licensed herein. As royalty payment obligations for an Agreement Product expire in a country, even if the Agreement thereafter remains in effect in such country, SPL, its Affiliates and Sublicensees, shall no longer have any remaining payment obligations hereunder with respect to such Agreement Product in that country.

10.2 Termination for Cause . This Agreement may be terminated by written notice by either Party at any time during the term of this Agreement if the other Party (the “Breaching Party”) is in material breach or default of any of its material obligations hereunder (including, without limitation, any payment obligations), as follows: (i) the terminating Party shall send written notice of the breach or default to the Breaching Party; and (ii) if such default or breach thereafter continues for sixty (60) days after written notice thereof was provided to the Breaching Party, then the termination shall become effective at the end of such sixty (60) day period, unless the Breaching Party (or any other party on its behalf) has cured any such breach or default prior to the expiration of the sixty (60) day period or has commenced activities reasonably expected to cure such breach within such sixty (60) day period and thereafter uses diligent efforts to complete the cure as soon as practicable.

10.3 Termination Upon Bankruptcy or Insolvency . This Agreement may be terminated by Pharmacopeia giving written notice of termination to SPL upon the filing of bankruptcy or insolvency of SPL or the appointment of a receiver for the assets of SPL, or the making by SPL of an assignment for the benefit of creditors, or the institution of any proceedings against SPL under any bankruptcy law. Termination shall be effective upon the date specified in such notice. The rights of SPL under this Agreement shall not terminate in the event of a bankruptcy of Pharmacopeia, unless SPL elects to terminate this Agreement in accordance with the following provisions of this Section 10.3. In the event that (i) Pharmacopeia shall make an assignment for the benefit of creditors, file a petition in bankruptcy, petition or apply to any tribunal for the appointment of custodian, receiver or any trustee for it or a substantial part of its assets, or shall commence any case or proceeding under any bankruptcy, reorganization, arrangement, readjustment of debt, dissolution or liquidation law or statute of any jurisdiction, whether now or hereafter in effect; or (ii) if there shall have been filed any such bona fide petition or application, or any such proceeding shall have been commenced against it, in which an order for relief is entered or which remains undismissed for a period of sixty (60) days or more; or (iii) if Pharmacopeia by any act or omission of act shall indicate its consent to, approval of or acquiescence in any such bona fide petition, application, or proceeding or order for relief or the appointment of a custodian, receiver or trustee for it or any substantial part of its property, or shall suffer any such custodianship, receivership or trusteeship to continue undischarged for a period of sixty (60) days or more (each such event a “Pharmacopeia Bankruptcy Event”), then SPL shall have the following rights. SPL shall have the right, in its sole discretion, to elect to terminate this Agreement by giving written notice of such termination to Pharmacopeia. In the event that SPL does not elect to terminate this Agreement, then notwithstanding any rejection of this Agreement by Pharmacopeia (which, for purposes of this Section 10.3, includes any debtor in possession, trustee or other entity that may succeed Pharmacopeia) pursuant to 11 U.S.C. §365, SPL shall retain all of its rights, benefits, licenses, protections and privileges under this Agreement and shall be entitled to all of the rights, benefits and protections of a licensee under 11 U.S.C. 365(n). SPL will have the right (including, without limitation, the right and ability to cure any and all defaults by Pharmacopeia under this Agreement, any agreement supplementary hereto, and any agreement with a Third Party affecting or comprising all or a part of the Pharmacopeia Technology, and to take any other actions, to oppose a rejection pursuant to 11 U.S.C. §365 of this Agreement, and to contract directly with Third Parties, if any, involved in contracted arrangements with Pharmacopeia with respect to performance of the Collaboration), provided that SPL’s obligations to make payments to Pharmacopeia under this Agreement shall automatically be reduced by the amount of all out-of-pocket costs and expenses incurred by SPL in exercising such rights. The Parties acknowledge and agree that all information, data and other intellectual property referred to in this Section 10.3 (including, without limitation, Pharmacopeia Technology) and all Agreement Compounds, Agreement Products, Collaboration Technology and any other intellectual property that is licensed, or is the subject of any other right, benefit, protection or privilege that is granted, transferred or otherwise afforded, to SPL hereunder is “intellectual property” within the meaning of 11 U.S.C. §365.

 

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10.4 Termination for Pharmacopeia Change in Control .

10.4.1 Termination of Entire Agreement . In the event of any Pharmacopeia Change in Control during the term of this Agreement, SPL shall have the right to terminate this Agreement upon ninety (90) days written notice after such Pharmacopeia Change in Control. In such event, the provisions of Sections 10.6.1, 10.6.2, 10.6.3 and 10.6.4(d) shall apply, but none of the provisions of Section 10.6.5 shall be applicable.

10.4.2 Termination of the Collaboration . In the event that such Pharmacopeia Change in Control occurs during the term of the Collaboration, SPL may, in its discretion, elect to terminate the Collaboration (but not the Agreement) on ninety (90) days written notice as set forth in Section 2.2.3. Upon receipt of written notice from SPL of its decision to terminate the Collaboration (but not the Agreement) pursuant to this Section 10.4.2 and Section 2.2.3, Pharmacopeia (or its successor in interest as a result of the Pharmacopeia Change in Control) shall have the option (exercisable in its sole discretion) to provide to SPL within thirty (30) days after receipt of such notice a written certification signed by a senior corporate officer of Pharmacopeia (or such successor) setting forth written representations and warranties by Pharmacopeia (or such successor):

 

  (i) that it is committed to continuing in good faith to perform the Collaboration under the terms of this Agreement;

 

  (ii) that it will continue to provide at least the same level and quality of personnel, facilities and resources for the performance of the Collaboration as existed prior to the Pharmacopeia Change in Control;

 

  (iii) that it will implement such additional safeguards as may be required (and which are reasonably acceptable to SPL) to ensure that all of SPL’s Confidential Information will be protected from unauthorized disclosure or use by Pharmacopeia (or such successor) and its Affiliates; and

 

  (iv) that it will take such other actions as are reasonably necessary to provide reasonable assurances to SPL that the results of the Collaboration, including without limitation, any Agreement Compounds and Collaboration Technology, will only be used by Pharmacopeia (or such successor) and its Affiliates in furtherance of the Collaboration or as otherwise expressly permitted under the terms and conditions of this Agreement.

If Pharmacopeia (or such successor) does not provide a certification under this Section 10.4.2 within such thirty (30) day period, then the Collaboration shall terminate upon expiration of the ninety (90) period following SPL’s notice of termination under this Section 10.4.2, and all of the provisions of Section 10.6.5 shall apply.

If Pharmacopeia (or such successor) does provide a certification under this Section 10.4.2 within such thirty (30) day period, then following SPL’s receipt of such certification from Pharmacopeia (or such successor) pursuant to this Section 10.4.2, SPL shall have the right to rescind its notice of termination of the Collaboration by providing written notice to Pharmacopeia within thirty (30) days after receipt of such written certification. If following receipt of such certification, SPL provides written notice rescinding its decision to terminate the Collaboration within such thirty (30) day period, then none of the provisions of Section 10.6 shall apply and the Collaboration shall continue under the terms and conditions of this Agreement as if SPL had never provided any notice of termination under Section 10.4.2. However, if following receipt of such certification, SPL does not provide written notice rescinding its decision to terminate the Collaboration within such thirty (30) day period, then the Collaboration shall terminate upon expiration of the ninety (90) day period following SPL’s notice of termination under Section 10.4.2, and the provisions of Section 10.6.5(i) and (ii) shall apply, but the provisions of Section 10.6.5(iii) shall not apply. For purposes of clarity and avoidance of doubt, the Parties agree that written notice provided by Schering Corporation rescinding a decision by Schering Corporation to terminate the Collaboration under the corresponding provisions of the US Agreement shall also be deemed notice by SPL under this Agreement.

 

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10.5 Concurrent Termination with the US Agreement . In the event of any termination of the US Agreement by either Pharmacopeia or Schering Corporation under the provisions of Sections 10.2, 10.3 or 10.4 thereof, as applicable, this Agreement shall automatically terminate concurrently under the corresponding Section 10.2, 10.3 or 10.4 of this Agreement.

10.6 Effect of Termination .

10.6.1 Accrued Obligations . Termination of this Agreement for any reason shall not relieve the Parties from any liability which at the time of such termination has already accrued to the other Party, or which is attributable to a period prior to such termination, nor preclude either Party from pursuing all rights and remedies it may have hereunder or at law or in equity with respect to any breach of this Agreement.

10.6.2 Return of Materials . Upon any termination of this Agreement, SPL and Pharmacopeia shall promptly return to the other Party all Confidential Information (including without limitation all Existing Schering Know-How or Existing Pharmacopeia Know-How, as the case may be) as set forth in Section 7.3.

10.6.3 Effect on Agreement Products . In the event that two (2) or more Agreement Compounds and/or Agreement Products are being developed and/or commercially exploited by SPL, its Affiliates or Sublicensees under this Agreement and a breach entitling Pharmacopeia to terminate this Agreement occurs which relates solely to a single Agreement Compound or Agreement Product, then Pharmacopeia shall have the option to terminate this Agreement only with respect to the applicable Agreement Compound or Agreement Product, and in which case all of the terms of this Agreement shall remain in full force and effect with regard to the other Agreement Compounds and/or Agreement Products being developed and commercialized. In the event this Agreement is terminated with respect to a given Agreement Product, SPL shall have the right to continue to sell its remaining inventory of such Agreement Product for a period of up to six (6) months after the date of termination, provided that SPL continues to pay royalties to Pharmacopeia with respect to such sales.

10.6.4 Licenses .

(a) Termination by Pharmacopeia Pursuant to Section 10.2 . In the event of termination by Pharmacopeia under Section 10.2, the licenses granted hereunder relating to any Agreement Product with respect to which there has been a material breach, shall terminate, and the licenses granted to Pharmacopeia hereunder shall remain in effect, subject to the terms and conditions of this Agreement; provided , however , a breach shall have no effect on SPL’s licenses hereunder other than with respect to the Agreement Product (together with any Hits, Lead Compounds which are Hits, and/or Derivative Compounds discovered by Pharmacopeia in performance of Screening Programs and/or Optimization Programs against the same Target as such Agreement Product) to which the breach specifically relates, and the remaining licenses granted hereunder shall remain in effect, subject to the terms and conditions of this Agreement.

(b) Termination by SPL Pursuant to Sections 10.2 or 10.3 . In the event of any termination by SPL pursuant to Section 10.2 or 10.3 above, any licenses granted by SPL hereunder shall terminate concurrently, and any licenses granted by Pharmacopeia shall remain in effect, subject to the terms and conditions of this Agreement.

(c) Termination by Pharmacopeia Pursuant to Section 10.3 . In the event of any termination by Pharmacopeia pursuant to Section 10.3 above, any licenses granted by Pharmacopeia hereunder shall terminate concurrently, and any licenses granted by SPL shall remain in effect, subject to the terms and conditions of this Agreement.

(d) Termination by SPL Pursuant to Section 10.4 . In the event of any termination by SPL pursuant to Section 10.4 above, any licenses granted by Pharmacopeia to SPL, and by SPL to Pharmacopeia, shall remain in effect, except for the licenses under Section 4.5, which shall terminate concurrently.

10.6.5 Effect of Termination of the Collaboration for Pharmacopeia Change in Control . In the event that the Collaboration (but not the Agreement) is terminated by SPL pursuant to Sections 10.4.2 and 2.2.3 as a result of a Pharmacopeia Change in Control, and the decision to terminate is not rescinded by SPL in accordance with Section 10.4.2, the Parties further agree that, effective as of *

 

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(i) the non-solicitation provisions of Section 11.8 shall not apply with respect to any of the individual Pharmacopeia employees identified as working on the Collaboration under Section 2.5.1;

(ii) to the extent that SPL contracts with one or more Third Parties to complete any Optimization Program which was ongoing at the time the Collaboration was terminated, SPL shall have the right to *

(iii) if (and only if) Pharmacopeia (or its successor in interest as a result of such Pharmacopeia Change in Control) has failed to timely provide a certification to SPL in accordance with Section 10.4.2, Pharmacopeia (or such successor)*

10.6.6 Surviving Provisions . Articles VI, VII, VIII, IX and XI of this Agreement, as well as Sections 2.9.2, 2.9.3, 2.10, 2.11, 4.1.3, 4.4, 4.7, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 5.10, and 10.6 shall survive the expiration or termination of this Agreement for any reason and shall remain in full force and effect.

ARTICLE XI

MISCELLANEOUS

11.1 Assignment . This Agreement shall not be assigned, or assignable, by either Party hereto to any Third Party without the prior written consent of the other Party, and any such attempted assignment shall be void and without force or effect; provided , however , that notwithstanding the foregoing, either Party may, without such consent, assign this Agreement and its rights and obligations hereunder to an Affiliate or in connection with the transfer or sale of all or substantially all of its business or assets related to the subject matter to which this Agreement pertains, or in the event of its merger, reorganization, acquisition, sale, consolidation or change in control or similar transaction. This Agreement shall be binding upon, and inure to the benefit of, each Party, its Affiliates, and its permitted successors and assigns. Each Party shall be responsible for the compliance by its Affiliates with the terms and conditions of this Agreement.

11.2 Governing Law . This Agreement and any dispute arising from the performance or breach hereof, shall be governed, interpreted and construed in accordance with the laws of the State of New Jersey, without giving effect to conflict of law principles. The Parties expressly exclude application of the United Nations Convention for the International Sale of Goods.

11.3 Dispute Resolution . Except as set forth in Sections 3.3 and 5.5.4, any dispute under this Agreement which is not settled by mutual consent shall be finally settled by binding arbitration, conducted in accordance with the Commercial Arbitration Rules of the American Arbitration Association by three arbitrators appointed in accordance with said rules. The arbitration shall be held in New York, New York and at least one of the arbitrators shall be an independent expert in pharmaceutical product development (including clinical development and regulatory affairs). Any written evidence originally in a language other than English shall be submitted in English translation accompanied by the original or a true copy thereof. The costs of the arbitration, including administrative and arbitrators’ fees, shall be shared equally by the Parties. Each Party shall bear its own costs and attorneys’ and witness’ fees. A disputed performance or suspended performances pending the resolution of the arbitration must be completed within thirty (30) days following the final decision of the arbitrators or such other reasonable period as the arbitrators determine in a written opinion. Any arbitration subject to this Section 11.3 shall be completed within one (1) year from the filing of notice of a request for such arbitration.

11.4 No Implied Licenses . Only the licenses granted pursuant to the express terms of this Agreement shall be of any legal force or effect. No license rights shall be created by implication, estoppel or otherwise.

11.5 Representation by Legal Counsel . Each Party hereto represents that it has been represented by legal counsel in connection with this Agreement and acknowledges that it has participated in the drafting hereof. In interpreting and applying the terms and provisions of this Agreement, the Parties agree that no presumption shall exist or be implied against the Party which drafted such terms and provisions.

 

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11.6 Waiver . Any delay or failure in enforcing a Party’ s rights under this Agreement or any waiver as to a particular default or other matter shall not constitute a waiver of such Party ’ s rights to the future enforcement of its rights under this Agreement, nor operate to bar the exercise or enforcement thereof at any time or times thereafter, excepting only as to an express written and signed waiver as to a particular matter for a stated duration.

11.7 Independent Contractors . The relationship of the Parties hereto is that of independent contractors. Nothing herein contained shall be deemed to create an employment, agency, joint venture or partnership relationship between the Parties hereto or any of their agents or employees. Neither Party shall have any power to enter into any contracts or commitments or to incur any liabilities in the name of, or on behalf of, the other Party, or to bind the other Party in any respect whatsoever.

11.8 Solicitation of Employees . SPL and Pharmacopeia both agree that, during the Collaboration Term and for one (1) year thereafter, without the express prior written consent of the other Party, they will not knowingly induce or attempt to induce, directly or indirectly, any scientific or technical personnel then employed by the other Party to accept employment or affiliation with the inducing Party or its Affiliates.

11.9 Compliance with Laws . In exercising their rights under this license, the Parties shall fully comply with the requirements of any and all applicable laws, regulations, rules and orders of any governmental body having jurisdiction over the exercise of rights under this license.

11.10 Export Control . This Agreement and the obligations of both Parties hereunder are made subject to, and limited by, all applicable restrictions concerning the export of products or technical information from the United States of America which may be imposed upon or related to Pharmacopeia or SPL from time to time by the government of the United States of America. Furthermore, SPL agrees that it will not export, directly or indirectly, any technical information acquired from Pharmacopeia under this Agreement or any products using such technical information to any country for which the United States government or any agency thereof at the time of export requires an export license or other governmental approval, without first obtaining the written consent to do so from the Department of Commerce or other agency of the United States government when required by an applicable statute or regulation.

11.11 Patent Marking . SPL agrees to mark and have its Affiliates and Sublicensees mark all Agreement Products sold pursuant to this Agreement in accordance with the applicable statute or regulations relating to patent marking in the country or countries of manufacture and sale thereof.

11.12 Notices . Any notice required or permitted to be given or sent under this Agreement shall be in writing and shall be hand delivered or sent by express delivery service or certified or registered mail, postage prepaid, or by facsimile transmission (with written confirmation copy by registered first-class mail) to the Parties at the addresses and facsimile numbers indicated below.

If to Pharmacopeia, to:

Pharmacopeia, Inc.

3000 Eastpark Boulevard

Cranbury, New Jersey 08512

Attn: Chief Executive Officer

Fax No.: (609) 452-3672

with a copy to:

Pharmacopeia, Inc.

3000 Eastpark Boulevard Cranbury,

New Jersey 08512

Attn: General Counsel

Fax No.: (609) 452-3655

 

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If to SPL, to:

Schering-Plough Ltd.

Toepferstrasse 5

CH 6004 Lucerne, Switzerland

Attention: President

Facsimile No.: (011) 41 41 418 1630

with copies to:

Schering Corporation

2000 Galloping Hill Road

Kenilworth, New Jersey 07033

Attention: Law Department, Senior Legal Director – Licensing

Facsimile No.: (908) 298-2739

Schering Corporation

2000 Galloping Hill Road

Kenilworth, New Jersey 07033

Attention: Vice President, Business Development

Facsimile No.: (908) 298-5379

Any such notice shall be deemed to have been given when received. Either Party may change its address or its facsimile number by giving the other Party written notice, delivered in accordance with this Section.

11.13 Force Majeure . Failure of any Party to perform its obligations under this Agreement (except the obligation to make payments when properly due) shall not subject such Party to any liability or place them in breach of any term or condition of this Agreement to the other Party to the extent (and only to the extent) that such failure is due to fire, explosion, flood, drought, war, terrorism, riot, sabotage, embargo, strikes or other labor trouble, failure of suppliers, a national health emergency, compliance with any order or regulation of any government entity acting with color of right, or any other cause beyond the reasonable control of such non-performing Party and not caused by the negligence, intentional conduct or misconduct of the non-performing Party (such event or cause referred to as “force majeure”). The Party affected shall promptly notify the other Party of the condition constituting force majeure as defined herein and shall exert reasonable efforts to eliminate, cure or overcome any such event of force majeure and to resume performance of its obligations with all possible speed. If a condition constituting force majeure as defined herein exists for more than ninety (90) consecutive days, the Parties shall meet to negotiate a mutually satisfactory resolution to the problem, if practicable. The foregoing notwithstanding, nothing herein shall require any Party to settle on terms unsatisfactory to such Party any strike, lock-out or other labor difficulty, any investigation or proceeding by any public authority or any litigation by any Third Party.

11.14 Severability . If any provision of this Agreement becomes or is declared by a court of competent jurisdiction to be illegal, invalid or unenforceable or void, it is mutually agreed that this Agreement shall remain in full force and effect without such provision, and the Parties will, in good faith, renegotiate the terms and conditions of this Agreement so as to lawfully include the substance of such provision (to the extent possible) in order to as fully as possible realize the intent of the Parties and their commercial bargain.

11.15 Counterparts . This Agreement may be executed in any number of counterparts, each of which shall be an original as against either Party whose signature appears thereon, but all of which taken together shall constitute but one and the same instrument, and shall become effective on the Effective Date.

11.16 Captions . The captions of this Agreement are solely for the convenience of reference and shall not affect its meaning or interpretation.

 

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11.17 Complete Agreement . This Agreement with its Exhibits, together with the US Agreement, constitutes the entire agreement between the Parties with respect to the subject matter hereof, and all prior agreements respecting the subject matter hereof, either written or oral, expressed or implied, shall be abrogated, canceled, and are null and void and of no effect; provided , however that except as expressly set forth in this Agreement, nothing herein shall affect the rights and obligations of the Parties under: (i) the certain Collaboration Agreement and the certain Random Library Agreement between Pharmacopeia, Schering Corporation and Schering-Plough Ltd. effective as of December 22, 1994, as amended (the “1994 Agreements”); or (ii) the certain contemporaneous Collaboration Agreements between Pharmacopeia and each of Schering Corporation and Schering-Plough Ltd., effective as of October 29, 1998, each as amended (the “1998 Agreements”). No amendment, modification, supplement, change or addition to this Agreement (or the Exhibits attached hereto) shall be effective or binding on either of the Parties hereto unless reduced to writing and executed by the respective duly authorized representatives of Pharmacopeia and SPL.

11.18 Relationship of Prior Agreements . For purposes of clarity and avoidance of doubt, the Parties acknowledge and agree that the terms and conditions of this Agreement shall not apply to any compounds or products discovered and developed by or on behalf of the Parties under the 1994 Agreements or the 1998 Agreements. In particular, the Parties acknowledge and agree that (i) no milestone payment or royalty obligations set forth in this Agreement shall apply to any compounds discovered and/or developed under the 1994 Agreements or the 1998 Agreements, and (ii) any Agreement Compounds and/or Agreement Products discovered and developed under this Agreement shall not be subject to any milestone payment or royalty obligations set forth in the 1994 Agreements or the 1998 Agreements.

11.19 Relationship to US Agreement; Controlling Provisions . The Parties acknowledge and agree that this Agreement together with the US Agreement are intended to operate together as a single worldwide agreement governing the rights and obligations of Pharmacopeia, SPL and Schering Corporation. For purposes of clarity and avoidance of doubt, the parties agree that Article II and Article III of this Agreement shall be subject to and governed by the corresponding provisions of the US Agreement. The Parties further agree that SPL’s rights and obligations with respect to the filing, prosecution, maintenance and enforcement of patents and patent applications under Article VI of this Agreement shall be exercised and performed by the employees and/or agents of Schering Corporation having responsibility for Schering Corporation’s rights and obligations under Article VI of the US Agreement, and that all such activities will be performed in a coordinated manner.

11.20 Recording . Each Party shall have the right, at any time, to record, register, or otherwise notify this Agreement in appropriate governmental or regulatory offices anywhere in the world, and each Party shall provide reasonable assistance to the other in effecting such recording, registering or notifying. The Parties acknowledge that this Agreement may be notified by either Party to the European Community for compliance with applicable laws.

11.21 Further Actions . Each Party agrees to execute, acknowledge and deliver such further instruments, and to do all other acts, as may be necessary or appropriate in order to carry out the purposes and intent of this Agreement including, without limitation, any filings with any antitrust agency which may be required.

 

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IN WITNESS WHEREOF, this Agreement has been executed by the duly authorized representatives of the Parties as of the date set forth below.

 

PHARMACOPEIA, INC.     SCHERING-PLOUGH LTD.
By:  

/s/    Stephen A. Spearman

    By:  

/s/    David Poorvin

Title:   EVP     Title:   Prokurist
Date:   7/9/03     Date:   7/9/03

 

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EXHIBIT A

CURRENCY CONVERSION


* EXHIBIT C

Elements of Fully Allocated Manufacturing Costs

The following expenses are included in manufacturing costs:

 

  1. Direct Materials

Materials used in the manufacturing process that are traced directly to the completed product, such as:

 

   

Inert raw materials or excipients

 

   

Active substances/ingredients

 

   

Packaging components such as bottles, caps, labels, etc.

 

  2. Direct Labor

The cost of employees engaged in production activities that are directly identifiable with product costs. Excludes supervision, which is included in indirect labor, and production support activities such as inspection, plant and equipment maintenance labor, and material handling personnel. Direct Labor cost includes:

 

   

Base pay, overtime, vacation and holidays, illness, personal time with pay, and shift differential.

 

   

Cost of employee fringe benefits such as health and life insurance, payroll taxes, welfare, pension, profit sharing and bonuses.

 

  3. Indirect Manufacturing Costs

Costs which are ultimately allocated to product based on an appropriate method such as standard direct labor hours, tank hours, grams, vials, etc., of the operating departments. These costs include:

 

   

Indirect Production Labor - salaries of employees engaged in production activities who are not classified as direct labor, including supervision, clerical, etc.

 

   

Costs of Direct Labor - employees not utilized for the manufacturing of product such as training, downtime and general duties.

 

   

Indirect Materials - supplies and chemicals which are used in the manufacturing process and are not assigned to specific products but are included in manufacturing overhead costs. Includes supplies for which direct assignment to products is not practical.

 

   

Utilities - expenses incurred for fuel, electricity and water in providing power for production and other plant equipment.

 

   

Maintenance and Repairs - amount of expense incurred in-house or purchased to provide services for plant maintenance and repairs of facilities and equipment.

 

   

Other Services - purchased outside services and rentals such as the cost of security, ground maintenance, etc.


   

Depreciation - of plant and equipment utilizing the straight-line method of calculation.

 

   

Insurance - cost of inventory insurance, comprehensive insurance and other insurance necessary for the safeguard of manufacturing plant and equipment.

 

   

Taxes - expense incurred for taxes on real and personal property (manufacturing site, buildings and the fixed assets of equipment, furniture and fixtures, etc.). If manufacturing site includes other operations (marketing, R&D, etc.), taxes are allocated to manufacturing on the basis of total real and personal property.

 

   

Cost of manufacturing, service departments - such as: (where applicable)

 

   

Packaging Engineering

 

   

Manufacturing Maintenance

 

   

Industrial Engineering

 

   

Receiving and Warehousing

 

   

Purchasing and Accounting

 

   

Production Scheduling

 

   

Inventory Management

 

   

Plant Materials Management

 

   

Central Weigh

 

   

Manufacturing Administration

 

   

Regulatory Affairs direct support to manufacturing (not to exceed $80,000 per year for a three(3) year period)

 

   

Allocated costs of services provided to manufacturing including: (where applicable)

 

   

Cafeteria

 

   

Personnel Operations

 

   

Health and Safety Services

 

   

Division Engineering and Operations Services

 

   

Plant Services (housekeeping)

 

   

Manufacturing Information Systems


   

Plant Power

 

   

Office of V.P. Manufacturing

Various bases are used for allocating these costs to manufacturing operating departments including headcount, square feet, metered utilities use, estimated services rendered, EDP computer hours, etc.

 

  4. Quality Assurance Costs

Direct labor and indirect costs for Quality Assurance departments testing and approving materials used in manufacturing and completed manufacturing batches and finished products. This includes all manufacturing in-process testing and testing of finished materials. Excluded from product costs are QA costs related to research and development, stability testing, etc.

The following expenses are not included in manufacturing costs:

 

  a) Inventory Carrying Costs

 

  b) Regulatory Affairs Costs (except as set forth above)

 

  c) Pilot plant costs, research batches and other similar costs prior to turnover to manufacturing. These are handled as development costs and expensed to R&D. This excludes commercial goods produced by a research facility.

 

  d) Costs incurred by Manufacturing for special projects, or for Schering-Plough Research Institute requests, to establish and certify new production processes, batch sizes and product line improvements, and new vendor certification of equipment and primary materials components. These costs are expensed to R&D.

 

  e) Manufacturing start-up costs and initial one-time extraordinary manufacturing costs incurred prior to plant operation and achievement of a normal production activity level. Includes costs of training, testing, qualification/validation of new equipment and facilities and initial trial batches. These costs are deferred and then amortized to Other Production Costs over five years.

 

  f) Significant idle capacity is eliminated from factory overhead and product cost. Idle or excess capacity costs are culled out of the Manufacturing Budget and expensed as a period cost to Other Production Costs.

 

  g) Finished goods warehousing, shipping and other distribution costs. These are included in distribution costs which are part of marketing expenses.

 

  h) Product liability and/or business interruption insurance expenses.

Exhibit 10.325

 

 

* CERTAIN INFORMATION IN THIS EXHIBIT HAS BEEN OMITTED AND FILED SEPARATELY WITH THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT TO THE OMITTED PORTIONS.

COLLABORATION AND LICENSE AGREEMENT

By and Between

PHARMACOPEIA, INC.

and

SCHERING CORPORATION


Table of Contents

 

i


COLLABORATION AND LICENSE AGREEMENT

This COLLABORATION AND LICENSE AGREEMENT (the “Agreement”), dated as of the latest date of signature appearing below (the “Execution Date”) and to be effective as of the Effective Date (as defined below), is made by and among: Pharmacopeia, Inc., a Delaware corporation having its principal place of business at 3000 Eastpark Boulevard, Cranbury, New Jersey 08512, (hereinafter referred to as “Pharmacopeia”); and Schering Corporation, a New Jersey corporation having its principal place of business at 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, U.S.A., (hereinafter referred to as “Schering”). Pharmacopeia and Schering are sometimes referred to herein individually as a Party and collectively as the Parties. References to “Schering” and “Pharmacopeia” shall include their respective Affiliates (as hereinafter defined).

WHEREAS, Schering and Pharmacopeia desire to collaborate to design and conduct medicinal chemistry optimization programs against Schering’s biological targets based upon lead compounds selected by Schering; and

WHEREAS, Schering and Pharmacopeia also desire for Pharmacopeia to conduct a separate program to identify new lead compounds by screening certain of its internal compound libraries for activity against biological targets selected by Schering; and

WHEREAS, Pharmacopeia and Schering’s Affiliate Schering-Plough Ltd. have entered into a collaboration and license agreement relating to countries and territories outside of the United States of even date herewith; and

WHEREAS, Schering and Pharmacopeia wish to modify and amend certain terms of the existing 1998 Agreements (as defined below) between the Parties related to Optimization Libraries (as defined in the 1998 Agreements);

NOW, THEREFORE, in consideration of the covenants, conditions, and undertakings herein contained, Schering and Pharmacopeia hereby agree as follows:

ARTICLE I

DEFINITIONS

As used in this Agreement, the following capitalized terms, whether used in the singular or plural, shall have the respective meanings set forth below:

1.1 “ Acceptance ” shall mean, with respect to an IND, NDA or HRD submitted by or on behalf of Schering or its Affiliate or Sublicensee, notice by the FDA (or an analogous regulatory authority in another country) that the IND, NDA or HRD has been accepted for review by the FDA (or analogous regulatory authority). In the event that the FDA (or analogous regulatory authority) is not required to provide such a notice of acceptance of an IND, NDA or HRD, then “Acceptance” shall be deemed to occur: (i) in the case of an IND, thirty (30) days following the date of submission, or if previously rejected any resubmission, of such IND; or (ii) in the case of an NDA or HRD, sixty (60) days following the date of submission, or if previously rejected any resubmission, of such NDA or HRD, unless in each case Schering or its Affiliates or Sublicensee receives notice from the FDA (or analogous regulatory authority), during the applicable thirty (30) or sixty (60) day period, that the NDA or HRD is not acceptable for review.

1.2 “ Activity Criteria ” shall mean the threshold criteria to be agreed upon by the Parties for identifying compounds having activity against the relevant Screening Target.

1.3 “ Affiliate ” shall mean any individual or entity directly or indirectly controlling, controlled by or under common control with, a Party to this Agreement. For purposes of this Agreement, the direct or indirect ownership of fifty percent (50%) or more of the outstanding voting securities of an entity, or the right to receive fifty percent (50%) or more of the profits or earnings of an entity shall be deemed to constitute control, or if not meeting the preceding requirements, any company owned or controlled by or owning or controlling Pharmacopeia or Schering at the maximum control or ownership right permitted in a country where such company exists. Such other relationship as in fact results in actual control over the management, business and affairs of an entity shall also be deemed to constitute control. *

 

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1.4 “ Agreement Compound ” shall mean any Lead Compound or Derivative Compound, as well as *

1.5 “ Agreement Product ” shall mean any product containing an Agreement Compound, including, without limitation, products for the therapeutic or prophylactic treatment or prevention of diseases and conditions in human beings or animals.

1.6 “ Carryover Programs ” shall have the meaning set forth in Section 2.02.

1.7 “ Collaboration ” shall mean the Optimization Programs and Screening Programs to be performed at Pharmacopeia’s facilities by Schering or Pharmacopeia under this Agreement to discover Agreement Compounds for further development by Schering.

1.8 “ Collaboration Committee ” shall have the meaning set forth in Section 3.1.

1.9 “ Collaboration Research Plan ” shall have the meaning set forth in Section 2.1.

1.10 “ Collaboration Target-Specific Technology ” shall mean Collaboration Technology relating to assays, compound screening methods and biological research tools, in each case which are discovered and developed through Collaboration research directed to a specific Target, or a small number of closely related Targets (e.g. a family of biological receptor subtypes), and are not readily applicable to other types of Targets; provided , however , that Collaboration Target-Specific Technology shall not include any rights in or to any Schering Technology (including, without limitation, Schering’s proprietary Targets) or any Agreement Compounds.

1.11 “ Collaboration Technology ” shall mean Collaboration Patent Rights and Collaboration Know-How.

1.11.1 “ Collaboration Patent Rights ” shall mean: (i) all patents and patent applications claiming any invention or discovery made by or on behalf of Pharmacopeia in performance of the Collaboration (including, without limitation, the synthesis and composition of matter of any Agreement Compound, or method of use thereof); and (ii) any divisions, continuations, continuations-in-part, reissues, reexaminations, extensions or other governmental actions which extend any of the subject matter of the patent applications or patents in (i) above, and any substitutions, confirmations, registrations, revalidations, or additions of any of the foregoing, in each case, which is owned or controlled, in whole or part, by license, assignment or otherwise by Pharmacopeia during the term of this Agreement; provided , however , that Collaboration Patent Rights shall not include any patents or patent applications which are Schering Technology or Pharmacopeia Technology.

1.11.2 “ Collaboration Know-How ” shall mean all proprietary ideas, inventions, data, know-how, instructions, processes, formulas, materials, expert opinion and information (including, without limitation, (i) biological, chemical, physical and analytical data and information relating to Agreement Compounds, and (ii) any structure-function data related to Lead Compounds or Derivative Compounds), in each case which is developed by Pharmacopeia in performance of the Collaboration; provided , however , that Collaboration Know-How shall not include Collaboration Patent Rights, Schering Technology or Pharmacopeia Technology.

1.12 “ Combination Product ” shall mean an Agreement Product which comprises two (2) or more active therapeutic ingredients at least one (1) of which is an Agreement Compound.

1.13 “ Derivative Compound ” shall mean any compound derived by Pharmacopeia in the performance of the Collaboration, in each case from one or more Lead Compounds, and having activity against the same Target as such Lead Compound(s). As used herein, a compound shall be deemed to have been “derived from” a Lead Compound if it *

 

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1.14 “ Development Candidate ” shall mean a Lead Compound, Derivative Compound or Schering Derivative which possesses the desirable properties of a therapeutic agent for the prevention or treatment of a clinical condition, in the absence of required safety trials necessary to begin human testing.

1.15 “ Effective Date ” shall have the meaning set forth in Section 2.01.

1.16 “ Excluded Compound ” shall have the meaning set forth in Section 2.9.3.

1.17 “ FDA ” shall mean the United States Food and Drug Administration or any corresponding foreign registration or regulatory authority.

1.18 “ First Commercial Sale ” shall mean, with respect to any Agreement Product, the first sale for end use of such Agreement Product in the Territory after receipt of the requisite Regulatory Approval.

1.19 “ FTE ” shall mean a full-time employee dedicated to the conduct of the Collaboration or, in the case of less than full-time dedication, a full-time equivalent person-year, based on a total of forty-six and one-fourth (46.25) weeks or one thousand eight hundred fifty (1,850) hours per year, of work on or directly related to the Collaboration.

1.20 “ Hit ” shall mean a Pharmacopeia Compound identified by Pharmacopeia during the term and in performance of the Collaboration as meeting the Activity Criteria with respect to the given Screening Target.

1.21 “ HRD ” shall mean a health registration dossier or its equivalent covering an Agreement Product filed in any country outside the United States and which is analogous to an NDA and including, where applicable, applications for pricing, pricing reimbursement approval, labeling and Regulatory Approval.

1.22 “ IND ” shall mean an Investigational New Drug application, as defined in the U.S. Food, Drug and Cosmetic Act and the regulations promulgated thereunder for initiating clinical trials in the United States, or any corresponding foreign application, registration or certification.

1.23 “ International Agreement ” shall mean that certain Collaboration and License Agreement entered into by and between Pharmacopeia and Schering-Plough, Ltd. of even date herewith.

1.24 “ Lead Compound ” shall mean any Hit or Schering Compound with respect to which the Parties agree to initiate a program of medicinal chemistry to identify a Development Candidate based upon the structure of such Hit or Schering Compound.

1.23 “ Major Market ” shall mean Japan or any three (3) of the following countries; France, Germany, Italy, Spain or the United Kingdom.

1.26 “ NDA ” shall mean a New Drug Application, Product License Application, or Biologic License Application, as defined in the U.S. Food, Drug and Cosmetics Act and regulations promulgated thereunder, or the equivalent filed with the FDA seeking approval to market and sell an Agreement Product in the United States.

1.27 “ Net Sales ” shall mean, with respect to each country in the Territory, the invoice price billed by Schering or its Affiliates, or their respective Sublicensees, to Third Parties (whether an end-user, a distributor or otherwise) for the sale of Agreement Products, and exclusive of intercompany transfers or sales among Schering, its Affiliates and/or Sublicensees in the Territory, less the reasonable and customary deductions from such gross amounts including: (i) normal and customary trade, cash and quantity discounts, allowances and credits; (ii) credits or allowances actually granted for damaged goods, returns or rejections of Agreement Product and retroactive price reductions; (iii) sales or similar taxes (including duties or other governmental charges levied on, absorbed or otherwise imposed on the sale of Agreement Product including, without limitation, value added taxes or other governmental charges otherwise measured by the billing amount, when included in billing); (iv) freight, postage, shipping, customs duties and insurance charges, when included in billing; (v) charge back payments and rebates granted to managed health care organizations or their agencies, and purchasers and reimbursers or to trade customers, including but not limited to, wholesalers and chain and pharmacy buying groups; (vi) commissions paid to Third Parties other than sales personnel and sale representatives or

 

3


sales agents; and (vii) rebates (or equivalents thereof) granted to or charged by national, state or local governmental authorities in a country in the Territory. In determining Net Sales of an Agreement Product any of the above discounts shall be accounted for and apportioned based on the list price of each such Agreement Product.

In the event that an Agreement Product is sold in the form of a Combination Product, Net Sales for such Combination Product will be calculated by multiplying actual Net Sales of such Combination Product by the fraction A/(A+B) where: A is the invoice price of the Agreement Product contained in the Combination Product if sold separately by Schering, an Affiliate or Sublicensee; and B is the invoice price of any other active therapeutic ingredients in the Combination Product if sold separately by Schering, an Affiliate or Sublicensee. In the event that the Agreement Product is sold in the form of a Combination Product containing one or more active therapeutic ingredients other than an Agreement Product and one or more such active therapeutic ingredients of the Combination Product are not sold separately, then the above formula shall be modified such that A shall be the fully allocated manufacturing cost to Schering, its Affiliates or Sublicensee of the Agreement Product and B shall be the fully allocated manufacturing cost to Schering, its Affiliate or Sublicensee of any other active therapeutic ingredients in the combination, in each case, determined in accordance with the schedule of fully allocated manufacturing costs set forth in Exhibit C.

1.28 “ Optimization Program ” shall mean a medicinal chemistry research program to discover one or more Development Candidates with respect to a given Target based upon one or more Lead Compounds.

1.29 “ Pharmacopeia Change in Control ” shall mean any of the following: (i) a reorganization, merger or consolidation of Pharmacopeia with a Major Pharmaceutical Company if the shareholders of Pharmacopeia (determined immediately prior to the reorganization, merger or consolidation taking effect) hold, directly or indirectly, less than fifty percent (50%) of the surviving corporation (determined immediately after such reorganization, merger or consolidation takes effect); (ii) an acquisition by a Major Pharmaceutical Company of direct or indirect beneficial ownership of voting stock of Pharmacopeia representing more than fifty percent (50%) of the total current voting power of Pharmacopeia then issued and outstanding; (iii) a sale of all or substantially all the assets of Pharmacopeia’s Drug Discovery division to a Major Pharmaceutical Company; or (iv) a liquidation or dissolution of Pharmacopeia. As used in this Section 1.29, the term “Major Pharmaceutical Company” shall mean any entity (including any corporation, joint venture, partnership or unincorporated entity), as well as any Affiliates or division(s) of such entity, that is engaged in the research, development, manufacturing, registration and/or marketing of drug products that are approved under NDAs, HRDs, ANDAs or Biologics License Applications, having total annual sales of pharmaceutical products of at least *

1.30 “ Pharmacopeia Compound ” shall mean a compound synthesized and characterized by Pharmacopeia and which is contained in one of Pharmacopeia’s proprietary internal compound libraries.

1.31 “ Pharmacopeia Technology ” shall mean Existing Pharmacopeia Patent Rights, Existing Pharmacopeia Know-How, and Pharmacopeia Improvements.

1.31.1 “ Existing Pharmacopeia Patent Rights ” shall mean (i) all patents and patent applications existing as of the Effective Date that claim the synthesis or composition of matter of a Lead Compound which is a Hit (and/or any other Hits from the same Screening Program as such Lead Compound) or a corresponding Derivative Compound, or the method of use thereof, and (ii) any divisions, continuations, continuations-in-part, reissues, reexaminations, extensions or other governmental actions which extend any of the subject matter of the patent applications or patents in (i) above, and any substitutions, confirmations, registrations, revalidations, or additions of any of the foregoing, in each case, which is owned or controlled, in whole or part, by license, assignment or otherwise by Pharmacopeia during the term of this Agreement, and subject to any limitations and prohibitions of such license or sublicense.

1.31.2 “ Existing Pharmacopeia Know-How ” shall mean all ideas, inventions, data, know-how, instructions, processes, formulas, expert opinion and information, including, without limitation, biological, chemical, physical and analytical data and information, existing as of the Effective Date, owned or controlled in whole or part by Pharmacopeia by license, assignment or otherwise, which is necessary for the discovery, development, manufacture or use of Lead Compounds based on Hits (and/or any other Hits from the same Screening Program as such Lead Compound) or corresponding Derivative Compounds and/or the discovery,

 

4


development, manufacture, use, sale or commercialization of corresponding Agreement Products, in each case, to the extent Pharmacopeia has the right to license or sublicense the same, and subject to any limitations and prohibitions of such license or sublicense.

1.31.3 “ Pharmacopeia Improvements ” shall mean all patentable inventions conceived and reduced to practice, solely or jointly, by Pharmacopeia or Schering in the conduct of the Collaboration that are within the scope of a claim of an issued patent within the Existing Pharmacopeia Patent Rights (i) which patent issued prior to the Effective Date or (ii) which claim has an effective filing date prior to the Effective Date; provided , however , that Pharmacopeia Improvements shall not include Pharmacopeia Independent Technology (as defined in Section 2.10.1).

1.32 “ Phase III ” shall mean Phase III clinical trials as prescribed by applicable FDA regulations, regardless of whether such trials are conducted in the United States or elsewhere.

1.33 “ Regulatory Approval ” shall mean any applications or approvals, including any INDs, NDAs, supplements, amendments, pre- and post-approvals, marketing authorizations based upon such approvals (including any prerequisite manufacturing approvals or authorizations related thereto) and labeling approval(s), technical, medical and scientific licenses, registrations or authorizations of any national, regional, state or local regulatory agency, department, bureau, commission, council or other governmental entity, necessary for the manufacture, distribution, use, import, export or sale of Agreement Product(s) in the Territory.

1.34 “ Schering Compound ” shall mean a compound which is independently discovered by or on behalf of Schering, without the use of Collaboration Technology or Pharmacopeia Technology as demonstrated by documented evidence created at the time of such discovery, and which is active against a specific Target.

1.35 “ Schering Derivative ” shall mean any compound derived by Schering during the term of the Collaboration or for a period of * after the expiration or earlier termination of the Collaboration, in each case from any Derivative Compound(s) or from a Lead Compound which is a Hit, and having as its primary mode of action *. As used herein, a compound shall be deemed to have been “derived from” such a Lead Compound or a Derivative Compound if it *

1.36 “ Schering Technology ” shall mean Schering Patent Rights, Schering Know-How and Schering Improvements.

1.36.1 “ Schering Patent Rights ” shall mean (i) all existing patents and patent applications owned or controlled in whole or in part by Schering or its Affiliates as of the Effective Date (including, without limitation, those which claim the synthesis or composition of matter of a Lead Compound or Derivative Compound, or the method of use thereof, or which relate to any Target or any assay provided by Schering for use in the Collaboration or the corresponding Targets for such assays), (ii) all patents and patent applications claiming any invention or discovery made by or behalf of Schering or its Affiliates, other than in performance of the Collaboration, in connection with the discovery and/or development of any Agreement Compounds and/or Schering Compounds, and/or the development and commercialization of any Agreement Product, and (iii) any divisions, continuations, continuations-in-part, reissues, reexaminations, extensions or other governmental actions which extend any of the subject matter of the patent applications or patents in (i) or (ii) above, and any substitutions, confirmations, registrations, revalidations, or additions of any of the foregoing.

1.36.2 “ Schering Know-How ” shall mean all ideas, inventions, data, know-how, instructions, processes, formulas, materials, expert opinion and information, including, without limitation, biological, chemical, pharmacological, toxicological, pharmaceutical, physical and analytical, clinical, safety, manufacturing and quality control data and information (except for any of the above arising in performance of the Collaboration) owned or controlled in whole or part by Schering by license, assignment or otherwise, which is necessary for the discovery, development, manufacture, use, sale or commercialization of Agreement Products, in each case, to the extent Schering has the right to license or sublicense the same, and subject to any limitations and prohibitions of such license or sublicense; provided , however , that Schering Know-How does not include Schering Patent Rights.

 

5


1.36.3 “ Schering Improvements ” shall mean all patentable inventions conceived and reduced to practice solely or jointly by Schering or Pharmacopeia in the conduct of the Collaboration that are within the scope of the claims of any issued patent within the Schering Patent Rights (i) which patent issued prior to the Effective Date or (ii) which claim has an effective filing date prior to the Effective Date.

1.37 “ Screening Program ” shall mean a program to screen Pharmacopeia’s internal compound libraries for activity against one or more Screening Targets for the purpose of identifying Hits.

1.38 “ Screening Target ” shall mean a Target agreed to by the Parties pursuant to Section 2.1.2.

1.39 “ Sublicensee ” shall mean with respect to a particular Agreement Product, a Third Party to whom Schering has granted a sublicense under the applicable Pharmacopeia Technology, Schering Technology or Collaboration Technology to make, use and/or sell such Agreement Product. As used in this Agreement, it is understood that “Sublicensee” shall also include a Third Party or Third Parties to whom Schering has granted the right to distribute such Agreement Product, provided that such Third Party or parties has (have) the primary responsibility for marketing and promotion at its (their) expense of such Agreement Product within the field or territory for which such distribution rights are granted, which marketing and promotional activities are not subsidized directly or indirectly by Schering.

1.40 “ Target ” shall mean a biomolecular entity (including, without limitation, receptors, enzymes, nucleic acids and proteins, and/or fragments thereof) that a small molecule is screened against in order to determine whether the small molecule demonstrates a specific biochemical or pharmaceutical effect.

1.41 “ Territory ” shall mean the United States and its territories, possessions and commonwealths.

1.42 “ Third Party ” shall mean any Party other than Pharmacopeia and its Affiliates, Schering and its Affiliates, Schering-Plough, Ltd. and its Affiliates, and their permitted assigns.

1.43 “ 1994 Agreements ” shall have the meaning set forth in Section 11.17.

1.44 “ 1998 Agreements ” shall have the meaning set forth in Section 11.17.

1.44 “ Valid Claim ” shall mean a composition-of-matter or method-of-use claim of an issued and unexpired patent included within the Collaboration Patent Rights or Pharmacopeia Patent Rights, and in each case which has not been revoked or held unenforceable or invalid by a decision of a court or other governmental agency of competent jurisdiction, unappealable or unappealed within the time allowed for appeal, and which has not been disclaimed, denied or admitted to be invalid or unenforceable through reissue or disclaimer or otherwise.

ARTICLE II

COLLABORATION

2.0 Effective Date; 1998 Agreements .

2.01 Effective Date . Schering and Pharmacopeia have signed this Agreement on the Execution Date as evidence of their mutual desire to establish a collaborative alliance to discover and develop Agreement Products effective against certain Targets. *

2.02 Relationship to 1998 Agreements . As of the Effective Date, all of Schering’s remaining obligations to provide research funding for Pharmacopeia FTEs under Sections 2.4 and 5.2 of the 1998 Agreements, and all of Pharmacopeia’s remaining obligations to provide FTEs under Section 2.5.1 of the 1998 Agreements, shall terminate. In addition, as of the Effective Date, any and all ongoing research programs at Pharmacopeia * shall continue to be performed using the Pharmacopeia FTEs to be provided under this Agreement, as determined by the Collaboration Committee. As of the Effective Date, any and all such ongoing programs (hereinafter “Carryover Programs”) shall be treated under this Agreement as Optimization Programs; provided , however , that notwithstanding anything herein to the contrary, the provisions of this Agreement related to diligence, milestone payments, royalties, ownership, exclusivity, patent related activities and any and all other rights or obligations with respect to * shall be governed by the

 

6


terms and conditions of the 1998 Agreements, and Schering shall have no milestone or royalty payment obligations under this Agreement with respect thereto. Except as expressly modified and amended by this Agreement, all other terms and conditions of the 1998 Agreements shall remain in full force and effect.

2.1 Collaboration Research Programs .

2.1.1 Optimization Programs . Within thirty (30) days of the Effective Date, the Collaboration Committee shall agree upon a written overall plan for each of the Optimization Programs to be conducted by the Parties (the “Collaboration Research Plan”). The Collaboration Research Plan shall be periodically revised and updated (at least annually) by the Collaboration Committee during the term of the Collaboration. The Collaboration Research Plan shall set forth the responsibilities of each of the Parties with respect to performance of the Optimization Programs. The Collaboration Committee shall have responsibility for monitoring the performance of Optimization Programs against the current Collaboration Research Plan. Notwithstanding the foregoing, the Parties acknowledge and agree that Schering, in its sole discretion, shall have primary responsibility and decision making authority with respect to the selection of the Targets and Lead Compounds and the specific Optimization Programs to be conducted during the Collaboration; provided that Pharmacopeia shall not be obligated to undertake an Optimization Program for a Target selected by Schering if Pharmacopeia reasonably determines that the performance of an Optimization Program based upon that Target would constitute a breach one or more of Pharmacopeia’s existing contractual obligations to Third Parties; and provided further , that Pharmacopeia’s obligation to undertake such an Optimization Program shall be subject to Section 2.12.

2.1.2 Screening Programs . Within thirty (30) days after the Effective Date, Schering shall notify Pharmacopeia in writing of the identity of * Screening Targets. Such notice shall include the applicable Activity Criteria recommended by Schering for each proposed Screening Target, which Activity Criteria shall constitute Schering Know-How. Such Activity Criteria shall include, without limitation, * Pharmacopeia shall have the right to reject any proposed Targets as Screening Targets if: (i) it has a pre-existing contractual obligation to any Third Party that provides for exclusivity and/or non-compete obligations with respect to such Target; or (ii) Pharmacopeia has previously screened one or more Pharmacopeia Compounds against the same Target and there are less than two million (2,000,000) Pharmacopeia Compounds that have not previously been screened against the Target; or (iii) in accordance with the terms of Section 2.12. In addition, in the event that Pharmacopeia reasonably believes (based upon objective scientific information) that the Activity Criteria recommended by Schering for a proposed Screening Target are not reasonably attainable, then the Collaboration Committee shall promptly meet to agree in good faith upon mutually acceptable Activity Criteria. Pharmacopeia shall promptly notify in writing whether it accepts or rejects each such Target as a Screening Target. Schering shall have the right to propose a replacement Target for each Target rejected by Pharmacopeia, which replacement Target may be accepted or rejected by Pharmacopeia, as described above. The Parties shall use reasonable efforts to agree on * Schering shall propose * additional Targets for acceptance by Pharmacopeia as Screening Targets for Screening Programs. Pharmacopeia shall have the right to accept or reject such Targets, as described above, and the Parties shall use reasonable efforts to agree on * new Screening Targets for Screening Programs to be conducted by Pharmacopeia * To the extent that Schering will be funding * the Parties shall use reasonable efforts to agree upon * new Targets (to be proposed by Schering * as Screening Targets for Screening Programs to be conducted by Pharmacopeia *

2.2 Collaboration Term . The term of the Collaboration shall be *and, unless extended pursuant to Section 2.2.1, or earlier terminated pursuant to Section 2.2.2 or Article X, shall expire on the third anniversary of the Effective Date.

2.2.1 Extension of Collaboration Term . In the event that Schering continues to fund the Collaboration *in accordance with Section 2.5.2, then the Collaboration may be extended for *as provided below. The first *shall be effective upon agreement by Schering *shall be effective upon agreement by Schering *Each of the *shall become effective upon written notice by Schering to Pharmacopeia that it agrees to the *in accordance with Section 2.8.3. *shall be at Schering’s sole discretion and shall be for the purpose of completing any Optimization Programs which are still in progress at the end *The *extension, if any, shall be effective upon written notice by Schering to Pharmacopeia at least* If Schering does not provide such notice, the Collaboration shall expire on *

 

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2.2.2 Wind Down Period . The parties acknowledge that * of the Collaboration is intended to serve as a wind down period during which any then ongoing Optimization Programs can be completed. Thus, if Schering does not elect to *during the * shall be the wind down period. In the event that Schering is * during * of the Collaboration and Schering does not agree to * during * of the Collaboration based upon one or more * then the Collaboration shall continue for a wind down period of * to enable the Parties to complete and wind down any remaining Optimization Programs then ongoing. Schering’s funding obligations during the * period shall be governed by the terms of Section 2.5.2 *2.5.4 *or 2.5.3 *, as applicable.

2.2.3 Termination of Collaboration Upon Pharmacopeia Change in Control . In the event of a Pharmacopeia Change in Control during the term of the Collaboration, Schering shall have the right, in its discretion, (i) to terminate the Agreement pursuant to Section 10.4.1, below, or (ii) to terminate the Collaboration and not the Agreement upon ninety (90) days written notice to Pharmacopeia after such Change in Control expressly stating its intention to terminate the Collaboration. In the event that Schering elects to terminate the Collaboration and not the Agreement, then (a) Schering will not be obligated to make the payments set forth in Section 5.2 for the period after the effective date of such termination, (b) Pharmacopeia shall not be obligated to conduct any Collaboration research activities after the effective date of such termination, and (c) the remaining terms and conditions of this Agreement, including without limitation the licenses and royalty obligations set forth herein, shall remain in full force and effect until the Agreement expires or is terminated as set forth in Article X, below.

2.2.4 Early Termination of Screening Programs . In the event that Pharmacopeia fails to identify any Hits meeting the applicable Activity Criteria from any of the Screening Programs conducted during * then Schering shall have the right to terminate all further obligations with regard to Screening Programs in *. This right shall be exercisable by Schering, in its sole discretion, by providing written notice to that effect to Pharmacopeia within * In the event that the Screening Programs are terminated pursuant to this Section 2.2.4, then Pharmacopeia shall not conduct any further Screening Programs under this Agreement during the remaining term of the Collaboration. In addition, notwithstanding anything herein to the contrary: (i) the Collaboration shall be limited to a total *of three (3) years with the third year being a wind down year in which Schering shall only be obligated to fund * chemists, as provided in Section 2.5.2; and (ii) the number of FTEs to be funded during *, consisting of * chemistry FTEs and * biology FTEs, to conduct the Optimization Programs * In the event that following such early termination of the Screening Programs by Schering, or during any other wind down period under Section 2.2.2, Pharmacopeia undertakes any new Optimization Programs based upon Lead Compounds which are Schering Compounds (“Wind Down Programs”), then notwithstanding anything herein to the contrary, Pharmacopeia shall be entitled to receive milestone payments with respect to any new Agreement Compounds resulting from such Wind Down Programs under Section 5.4.1(a), but shall not be entitled to receive any royalty payments under Section 5.5 on sales of any Agreement Products containing an Agreement Compound resulting from such Wind Down Programs or with respect to any pharmaceutical products containing a Schering Compound having primary activity against the Target which was the subject of the Wind Down Program.

2.3 Pharmacopeia Responsibilities . Pharmacopeia shall use commercially reasonable efforts to provide:

(i) the number of scientist FTEs agreed to by the Parties, as set forth in Section 2.5, and such additional scientists as may be mutually agreed to in writing by the Parties and paid for by Schering, for performance of the Collaboration during each year of the Collaboration (it being understood and agreed that FTEs provided by Pharmacopeia for the Collaboration under the International Agreement shall also be deemed to be provided to this Collaboration for purposes of determining the number of FTEs provided by Pharmacopeia hereunder);

(ii) research facilities, laboratories and equipment sufficient to enable the Collaboration scientists (including Pharmacopeia employees and one (1) Schering employee to be provided pursuant to Section 2.4(i)) to perform the Collaboration in a fashion similar to the operation of Pharmacopeia’s own operations. The chemistry FTEs shall work in dedicated laboratories at Pharmacopeia’s research facilities in New Jersey; and

(iii) administrative services necessary to conduct the business of the Collaboration in a manner comparable to that of Pharmacopeia’ s own business activities.

 

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It is understood and agreed that, except as may be mutually agreed by the Parties, Pharmacopeia shall not be obligated hereunder to conduct research or development activities in the Collaboration which are outside the scope of the Collaboration Research Plan or the Screening Programs.

2.4 Schering Responsibilities . Schering shall provide research funding for the Collaboration as set forth in Section 5.2 and shall use commercially reasonable efforts to provide:

(i) one scientific director provided by Schering, in combination with Schering-Plough, Ltd., to work full-time on the Collaboration managing the day-to-day operations of the Collaboration (the “Collaboration Director”);

(ii) additional support for Collaboration research projects, including, without limitation, scientists, facilities and materials to perform biological research to identify Targets, assay development, compound screening, medicinal chemical research and analytical support services; and

(iii) the research materials, procedures and Schering Know-How necessary to conduct the Screening Programs, as provided in Section 2.8.

2.5 Collaboration Staffing .

2.5.1 Pharmacopeia Initial FTE Commitments . During * Pharmacopeia will provide * FTEs, consisting of synthetic/medicinal chemists * and the remaining * biology FTEs to be allocated, as determined by the Collaboration Committee, between bioassay support for Optimization Programs and performance of Screening Programs. The Parties agree that the Collaboration Committee shall have the right to (i) increase or decrease the total number of FTEs to be provided by Pharmacopeia and funded by Schering during any year of the Collaboration, and/or (ii) to adjust the allocation of the total number of FTEs working on the Collaboration between chemistry and biology FTEs, in each case as necessary to carry out the Collaboration Research Plan; provided , however , that any such adjustments must be agreed upon by the Collaboration Committee in advance in writing, shall not be made more than once in any given quarter, and shall not * or * in any wind down year. Pharmacopeia’s obligation to provide FTEs during * as well as during any extension of the Collaboration pursuant to Section 2.2.1 or wind down period pursuant to Section 2.2.2, shall be determined in accordance with Sections 2.5.2, 2.5.3 or 2.5.4, as applicable. All of the Pharmacopeia chemistry FTEs assigned to work on the Collaboration * On or before the Effective Date, Pharmacopeia will provide to Schering a list individually identifying those Pharmacopeia chemistry FTEs assigned to the Collaboration, which list shall be updated from time to time during the term of the Collaboration as FTEs assigned to work exclusively for the Collaboration are added, removed and/or replaced. During the term of the Collaboration, upon initiating each Optimization Program, Pharmacopeia will also individually identify a biology FTE as the primary contact at Pharmacopeia for the performance of assays and other biology related activities for such Optimization Program, it being understood that such individuals may have responsibility for more than one Optimization Program. It is understood that, in the aggregate, the education, training and experience levels of all Pharmacopeia FTEs assigned to the Collaboration will be reasonably representative of Pharmacopeia employees working on Pharmacopeia’s internal research programs. Within fifteen (15) business days after the Effective Date, Pharmacopeia will provide Schering with: (i) a copy of the Collaboration Business Conduct Policy (as described in Section 7.6) to be observed by all Pharmacopeia FTEs assigned to work on the Collaboration; and (ii) Pharmacopeia’s written representation and warranty that all such FTEs assigned to the Collaboration have read and understand the terms of the Collaboration Business Conduct Policy.

2.5.2 Pharmacopeia FTE Commitments for *. In the event that during *the Parties have initiated, or Schering has agreed to initiate, * Optimization Programs * then Pharmacopeia shall continue to provide, and Schering will continue to fund, * FTEs during *If at least * then Schering shall have the right (in its sole discretion) to reduce the number of FTEs to be provided by Pharmacopeia and funded by Schering; provided that the number of Pharmacopeia FTEs to be funded by Schering during the third year of the Collaboration shall be * FTEs; and provided further that all such FTEs shall be chemistry FTEs dedicated to work full time on the Collaboration.

2.5.3 Pharmacopeia FTE Commitments During * . If the term of the Collaboration is * pursuant to Section 2.2.1, Schering shall continue to fund and Pharmacopeia shall continue to provide * FTEs during *, if applicable. If Schering extends the Collaboration for * pursuant to Section 2.2.1, then the level of FTE support to be provided by Pharmacopeia and funded by Schering shall be determined by the Parties based * to be completed during *.

 

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2.5.4 Pharmacopeia FTE Commitments * . Schering shall have the right (in its sole discretion) to decrease the level of FTE support to be provided by Pharmacopeia and funded by Schering * as determined pursuant to Section 2.2.2) * provided that the number of Pharmacopeia FTEs to be funded by Schering during * shall be at least *; and provided further that all such FTEs shall be chemistry FTEs dedicated to work full time on the Collaboration.

2.5.5 Schering FTE Commitments . During the term of the Collaboration Schering shall, in combination with Schering-Plough Ltd. under the International Agreement, provide a single scientific director as set forth in Section 2.4(i). Such director shall be subject to Pharmacopeia’s confidentiality restrictions such as limited access to laboratories and access only to data that specifically relate to the Collaboration. It is understood that the scientific director shall remain an employee of Schering, and that Schering shall remain responsible for, and indemnify Pharmacopeia for any claims arising from or relating to, the conduct, activities, salary and benefits of such director, except to the extent caused by the gross negligence or willful misconduct of Pharmacopeia. In addition, Schering shall provide such additional FTEs located at Schering’s research facilities as Schering determines, in its sole discretion, are reasonably necessary to support the ongoing research programs of the Collaboration, including, without limitation, assay development, screening, medicinal chemistry, analytical services and animal testing services.

2.6 Capital Expenditures . In the event that the Parties reasonably determine that one or more Optimization Programs to be performed at Pharmacopeia, as identified in the applicable Collaboration Research Plan, will require capital expenditures to provide Pharmacopeia with access to specialized equipment needed to perform such Optimization Program, Schering shall be responsible (at its expense) for the purchase of such specialized equipment, and for purchasing, or reimbursing Pharmacopeia for the out-of-pocket costs of, any specialized consumables that are uniquely necessary for the proper operation of such specialized equipment. The Parties will make arrangements for the delivery and installation of such specialized equipment at Pharmacopeia’s facilities; provided that the specialized equipment is and shall remain the sole and exclusive property of Schering. Pharmacopeia shall have the right to utilize the specialized equipment in performance of Optimization Programs and shall not use the specialized equipment for any other activities or programs whatsoever. Pharmacopeia shall be responsible (at its own expense) for all routine operating costs incurred in connection with the use of any specialized equipment provided by Schering under this Section 2.6, including without limitation, any utility costs and the costs of reagents, solvents or other supplies necessary for the operation of the specialized equipment. Pharmacopeia shall ensure that all Pharmacopeia employees operating the specialized equipment have been properly trained in its use and shall use the specialized equipment in accordance with the instructions and operating procedures to ensure its proper use. Pharmacopeia shall be responsible (at its expense) for any damage (excluding ordinary wear and tear) to any of Schering’s specialized equipment provided to Pharmacopeia pursuant to this Section 2.6 resulting from Pharmacopeia’s use of the specialized equipment. Upon expiration or earlier termination of the Collaboration, Pharmacopeia shall fully cooperate with Schering to promptly return the specialized equipment to Schering. Alternatively, the Parties may decide to permit Pharmacopeia to retain the specialized equipment following the expiration or termination of the Collaboration, in which case the Parties shall arrange for the purchase and transfer of ownership of the specialized equipment to Pharmacopeia on financial terms to be agreed to by the Parties based upon the then current fair market value of the specialized equipment.

2.7 Record Keeping and Inspection of Records . Each of Schering and Pharmacopeia, and their respective Affiliates, shall maintain records of its Collaboration activities (or cause such records to be maintained) in sufficient detail and in good scientific manner appropriate for patent and regulatory purposes as will properly reflect all work performed and the results achieved in performance of the Collaboration. Schering shall also maintain analogous records of its development activities with respect to Agreement Compounds and Agreement Products. Such records may include books, records, reports, research notes, charts, graphs, comments, computations, analyses, recordings, photographs, computer programs and documentation thereof, computer information storage media, samples of materials and other graphic or written data generated in connection with the Collaboration, including any data required to be maintained pursuant to all requirements of applicable laws, rules and regulations, or as directed by the Collaboration Committee. Pharmacopeia’s records shall also document by name which individuals assigned to the Collaboration

 

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pursuant to Section 2.5 are working on each specific Collaboration research project (identifying the Target(s) involved). During the Collaboration and for five (5) years thereafter, each of Schering and Pharmacopeia shall have the right, upon at least five (5) business days’ prior notice, to inspect all such records of the other Party (or legible copies thereof) during normal business hours. Each Party’s rights under this Section 2.7 shall be limited to one (1) inspection in any calendar year. In each case, the Party conducting the inspection shall maintain such records and the information disclosed therein in confidence in accordance with Section 7.1, and shall use such information solely for purposes of this Agreement. Upon request and tender of payment for the actual cost in providing copies, Pharmacopeia and/or Schering, as appropriate, shall provide to the requesting Party copies of such records.

2.8 Performance of Screening Programs . With respect to each Screening Target, the Parties agree that promptly following the acceptance by Pharmacopeia of each Screening Target in accordance with Section 2.1.2, Schering will provide Pharmacopeia (free of charge) with reasonable quantities of the Screening Target protein and any of Schering’s other proprietary reagents required to perform assays to identify compounds having activity against such Screening Target. All such proteins and other reagents are and shall remain the property of Schering, shall be used by Pharmacopeia solely in performance of the Screening Program, and shall not be transferred or otherwise made available to any Third Party without Schering’s prior written consent (which consent may be granted or withheld in Schering’s sole discretion.) Upon receipt of such * Pharmacopeia shall use diligent efforts to initiate and conduct a Screening Program to identify Pharmacopeia Compounds having activity against such Screening Target. Such efforts shall include any assay development work or assay modifications necessary to enable Pharmacopeia to perform the relevant assays to determine whether or not the applicable Activity Criteria are met for such Screening Target. Except as otherwise provided in Section 2.6, Pharmacopeia shall be solely responsible * Effective upon acceptance by Pharmacopeia of each Screening Target under Section 2.1.2, Pharmacopeia shall not conduct any screening of Pharmacopeia Compounds, either for itself or for any Third Party, against the same Target as such Screening Target (as determined pursuant to Section 2.11.1) for the period *

2.8.1 Hits . Any Pharmacopeia Compound(s) identified as meeting the Activity Criteria against a Screening Target through screening of the Pharmacopeia Compounds by Pharmacopeia during the term of the Collaboration, shall be designated a Hit. Upon completion by Pharmacopeia of the Screening Program for a given Screening Target, Pharmacopeia shall promptly notify Schering of all Hits identified with respect to that Screening Target, which notice shall identify the Screening Target and the available data generated by Pharmacopeia regarding *but shall not disclose the chemical structure of the Hits, or in the event that no Hits are identified from the Screening Program, Pharmacopeia shall notify Schering to that effect. * information and samples of Hits solely for the purpose of confirming that such Pharmacopeia Compound meets the Activity Criteria for the Screening Target. This will include the performance by Schering of any tests necessary to confirm * Schering agrees, however, not to conduct, or have conducted, *

2.8.2 * Within Schering shall notify Pharmacopeia in writing of those compounds which Schering has confirmed are Hits * Promptly after receipt of such notice, Pharmacopeia shall disclose to Schering * Upon receipt of the * Schering shall ensure that those employees having access to the * shall only use such information for *

2.8.3 Lead Compounds from Screening Programs . * Schering shall notify Pharmacopeia which (if any) of those confirmed Hits are acceptable to Schering as Lead Compounds for initiation of new Optimization Programs. Following notice from Schering that one or more Hits are acceptable as Lead Compounds, the Parties shall, as soon as reasonably practicable, initiate a new Optimization Program based upon such Lead Compound(s) in accordance with Section 2.9. The Parties acknowledge and agree that if Schering notifies Pharmacopeia that at least one Hit is acceptable to Schering as a Lead Compound for a given Screening Target, then the licenses granted to Schering under Article 4 with respect to such Lead Compound shall also include * The restrictions set forth in Section 2.8.2 regarding disclosure, access and use of structural information with respect to confirmed Hits shall no longer apply following notice of acceptance by Schering of one or more such Hits as a Lead Compound pursuant to this Section 2.8.3. Upon acceptance by Schering of one or more Hits as a Lead Compound pursuant to this Section 2.8.3, the duration of the restriction on screening by Pharmacopeia against the relevant Screening Target, as set forth in the last sentence of Section 2.8, *

 

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2.8.4 Hits Not Accepted by Schering . In the event that Schering does not accept any of the Hits identified by Pharmacopeia with respect to a given Screening Target as Lead Compounds for an Optimization Program, Pharmacopeia shall have the right to * In the event that Pharmacopeia decides to * Following receipt of any * by Schering, the Parties agree that for *

2.9 Performance of Optimization Programs . The first Optimization Programs to be performed under this Agreement are the ongoing research programs for Optimization Libraries (as defined in the 1998 Agreements) listed in Exhibit D, which shall be subject to the terms and conditions of Section 2.0. All new Optimization Programs to be initiated by the Parties after the Effective Date shall be programs based upon Lead Compounds selected under the terms and conditions of this Agreement and Section 2.0 shall not apply to any such new Optimization Programs. It is anticipated that the Parties will generally seek to maintain * ongoing Optimization Programs during each year of the Collaboration in which Schering is funding research at the full level of * FTEs in accordance with Section 2.5; provided , however , that the Parties acknowledge that the actual number of ongoing Optimization Programs at any given time may vary and shall be subject in part to Pharmacopeia’s success in identifying Hits from Screening Programs. If the Parties are unable to maintain * of Optimization Programs based upon Lead Compounds which are Hits from Screening Programs, Schering will use commercially reasonable efforts to approve and initiate new Optimization Programs based upon Lead Compounds which are Schering Compounds as necessary in order maintain a reasonable number of ongoing Optimization Programs based upon the available Pharmacopeia FTEs working on the Collaboration; provided , however , failure by Schering to provide Lead Compounds which are Schering Compounds shall not constitute a breach under this Agreement. If Schering ceases funding the Collaboration at the full level in * in accordance with Sections 2.5.2, 2.5.3 and 2.5.4, then Schering will not be obligated to initiate any new Optimization Programs *. The Collaboration Committee shall be responsible for allocation of the FTEs and other resources among the various Optimization Programs selected by Schering. This will include allocation of the medicinal chemistry FTEs, as well as additional FTEs to provide bioassay support, as necessary, for each Optimization Program to generate primary assay data for Lead Compounds and Derivative Compounds. In the event that all FTEs are fully allocated among the various ongoing Optimization Programs, any new Optimization Programs will be initiated as resources become available within the Collaboration, based upon prioritization determined by Schering. Any delay in initiating an Optimization Program based upon a Lead Compound which is a Hit from a Screening Program shall not have any effect on the acceptance of such Hit as a Lead Compound and Pharmacopeia shall not acquire any *

2.9.1 Preparation of Derivative Compounds . In performing each Optimization Program, Pharmacopeia shall undertake the synthesis of analogs and other Derivative Compounds based upon the relevant Lead Compounds. Pharmacopeia will also conduct primary screening assays of all such Derivative Compounds to determine activity against the applicable Target. Pharmacopeia will provide the Collaboration Committee with regular (at least quarterly) written reports of the data and results generated in performance of each Optimization Program. Such reports will identify the chemical structure of any and all Derivative Compounds prepared by Pharmacopeia in performance of the Optimization Program (whether or not such compounds are identified as active against the Target), and all test data with respect thereto.

2.9.2 * .

2.9.3 * Notwithstanding the provisions of Section 2.9.2, *

2.9.4 Leads Based Upon Schering Compounds . Schering shall not be obligated to disclose the structure of any Schering Compound(s) proposed as Lead Compounds unless and until Pharmacopeia has agreed, pursuant to Section 2.1.1, to conduct an Optimization Program against the relevant Target. Upon Pharmacopeia’s agreement to conduct an Optimization Program based upon one or more Lead Compounds which are Schering Compounds, Schering shall disclose to Pharmacopeia the structure of such Schering Compounds. Effective upon the date Pharmacopeia agrees to perform an Optimization Program based upon one or more Lead Compounds which are Schering Compounds, for the period extending from *

2.10 Pharmacopeia Independent Research Activities .

2.10.1 Activities Outside the Collaboration . The Parties acknowledge that during and after the term of the Collaboration Pharmacopeia may (either alone or in collaboration with one or more Third Parties) perform independent research and development

 

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activities with respect to Targets (including, without limitation, to identify, develop and commercialize products), which activities are not within the scope of this Agreement; provided that Pharmacopeia shall not use any Schering Technology, and except as otherwise expressly set forth in this Agreement shall not use any Collaboration Technology, in connection with any such independent research and development activities. Any data, information, materials, compounds, products or other technology resulting from such independent research and development activities is the property of Pharmacopeia (“Pharmacopeia Independent Technology”). The Parties further acknowledge that Pharmacopeia Independent Technology may include technology independently acquired, discovered or developed by Pharmacopeia (as demonstrated by documented evidence created at the time of such acquisition, discovery or development) and which coincidentally is substantially the same as technology within the scope of Collaboration Technology and/or Schering Technology. Schering shall have no rights or licenses whatsoever to any Pharmacopeia Independent Technology.

2.11 Schering’s Screening Programs . The Parties acknowledge that Schering shall have the right to conduct its own independent screening programs against any and all Targets, and that except as expressly set forth in this Section 2.11, * resulting from such independent screening programs. Schering shall have the right * The Parties acknowledge and agree that any pharmaceutical products discovered, developed and commercialized as a result of * are and shall be treated as Agreement Products and shall be subject to * but shall not be subject *

2.11.1 Differentiation of Targets . A Target will encompass *

2.12 Third Party Patents . The Parties acknowledge and agree that Pharmacopeia shall have the right to reject and shall not be obligated to undertake any Screening Program or Optimization Program, or any new research activities in connection with an ongoing Screening Program or Optimization Program, pursuant to this Agreement if Pharmacopeia reasonably determines, in good faith, that such program or activities cannot be performed without infringing an issued US patent held by a Third Party. It is further understood and agreed that, unless Schering obtains a license for Pharmacopeia, or grants Pharmacopeia a sublicense under a license held by Schering, to conduct such program or research activities, Pharmacopeia’s failure to conduct such program or research activities shall not constitute a breach of this Agreement. Pharmacopeia shall promptly inform Schering in the event that Pharmacopeia determines in accordance with this Section 2.12 that it will be unable to undertake any proposed Screening Program, Optimization Program or research activities due to Third Party patents. *

ARTICLE III

COLLABORATION MANAGEMENT

3.1 Collaboration Committee . The Parties shall establish a Collaboration Committee to oversee, review and coordinate the conduct of the Collaboration. The Collaboration Committee shall be comprised of three (3) representatives from each of Schering and Pharmacopeia, or such other equal number of representatives as the Parties may agree, each Party’s members selected by that Party. Each of Pharmacopeia and Schering may replace its Collaboration Committee representatives at any time upon written notice to the other Party. The Collaboration Committee shall be chaired by the Collaboration Director appointed by Schering, unless otherwise agreed by the Parties.

From time to time the Collaboration Committee may establish various subcommittees, constituted as agreed by the Collaboration Committee, to oversee particular projects or activities within the Collaboration.

3.2 Collaboration Committee Meetings . During the term of the Collaboration, including as it may be extended, the Collaboration Committee shall meet at least four (4) times per year, or more often as agreed by the Parties, at such locations as the Parties shall agree. At such meetings the Collaboration Committee’s responsibilities will include: (i) formulating and reviewing the Collaboration objectives with respect to each Optimization Program; (ii) monitoring the progress of the Collaboration toward those objectives; (iii) evaluating Hits identified by Pharmacopeia from Screening Programs; (iv) initially reviewing recommendations by Pharmacopeia to Schering for Hits proposed to be accepted as Lead Compounds for new Optimization Programs; and (v) taking such other actions as may be specified under this Agreement or which the Parties deem appropriate. The Collaboration Committee may designate a patent committee comprised of employees or representatives of the Parties to oversee the patent prosecution and/or enforcement activities described in Article VI, and to facilitate communication and agreement between the Parties regarding inventorship of

 

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inventions made in the Collaboration and the classification of such inventions (e.g., as Schering Improvements, Pharmacopeia Improvements, Collaboration Technology, etc.). Additional non-voting representatives or consultants from either Party may from time to time be invited by Schering or Pharmacopeia to attend and participate in Collaboration Committee meetings (e.g., to evaluate and advise on business or scientific issues) subject to compliance with the confidentiality provisions of Section 7.1. Each Party shall be responsible for its own expenses in connection with the Collaboration Committee.

3.3 Collaboration Committee Decisions . Decisions of the Collaboration Committee shall be based upon the consensus of all the members. In the event that the Collaboration Committee cannot or does not, after good faith efforts, reach agreement on an issue, such issue shall be referred to the President of Schering’ s Affiliate, the Schering-Plough Research Institute (“SPRI”), and the President and Chief Operating Officer of Pharmacopeia Drug Discovery for resolution. In the event that these officers are unable to resolve the issue within fifteen (15) business days after submission of the issue to them, then the unresolved issue may be submitted by either Party to binding arbitration pursuant to Section 11.3 of this Agreement, except that the decision shall be made by one (1) arbitrator with expertise in pharmaceutical product development, and the decision of the arbitrator shall be rendered within six (6) months of initiation of the arbitration. During the pendency of any such arbitration proceedings, the Parties shall proceed with performance of the Collaboration following the course of conduct determined by Schering; provided , however , that notwithstanding the foregoing, Pharmacopeia shall not be obligated to (i) perform any action that would violate its obligations to any Third Party or contravene Section 2.12, (ii) spend or forego receiving any amounts of money (except as necessary in connection with the fulfillment of Pharmacopeia’s responsibilities under Section 2.3), or (iii) knowingly prepare or deliver to Schering any compounds previously licensed to any Third Party. Notwithstanding the foregoing, Schering, in its sole discretion, shall have complete and final control over Schering’s research, development and commercialization of Schering Compounds, Agreement Compounds and/or Agreement Product(s) in accordance with the terms and conditions of this Agreement.

3.4 Development Status; Notice of Sale of Agreement Products . During the term of this Agreement, Schering shall provide Pharmacopeia written annual reports within thirty (30) days after the first and each subsequent anniversary of the Effective Date, which reports shall provide: (i) a brief report summarizing the development status of each Lead Compound and/or Development Candidate under development at Schering; (ii) the status of all patent applications claiming any Library Compounds or Derivative Compounds, and (iii) copies of all such patent applications which have published during the relevant twelve (12) month period and were not previously provided to Pharmacopeia. Such reports shall contain information sufficient to allow Pharmacopeia to monitor the status of Schering’s efforts with respect to the accomplishment of the milestones set forth in Section 5.3; provided , however , that nothing hereunder shall be construed as requiring Schering to provide Pharmacopeia with any specific research data or results, including, without limitation, information relating to Targets or data obtained from screening programs being conducted at Schering. Until the First Commercial Sale of each Agreement Product by or on behalf of Schering hereunder, Schering shall keep Pharmacopeia reasonably informed as to the status of the pre-clinical, clinical and commercial development of such Agreement Product by providing Pharmacopeia with annual written reports summarizing such activities with respect to each potential Agreement Product under development during the term of this Agreement. Within thirty (30) days of the First Commercial Sale of any Agreement Product, Schering shall give Pharmacopeia written notice thereof, which notice shall describe the relevant Agreement Product, identify the active ingredients in such Agreement Product, and identify the specific Target(s) which led to the development of such Agreement Product.

3.5 Diligence . The Parties acknowledge and agree that all business decisions regarding research, development and commercialization of Agreement Products (including, without limitation, decisions relating to the development and manufacture of Agreement Compounds, or to the design, development, manufacture, sale, price, distribution, marketing and promotion of Agreement Products under this Agreement) and the decision whether to develop (or cease developing) a particular Agreement Compound, or to develop and commercialize (or cease developing and commercializing) a particular Agreement Product, shall be within the sole discretion of Schering. Schering shall use reasonable good faith efforts to discover and develop Agreement Compounds, and to discover, develop and commercialize Agreement Products; provided , however , that Schering shall have no quotas or other minimum diligence obligations with regard to number of Agreement Compounds and Agreement Products to be developed and commercialized hereunder. Such decision making and/or reasonable good faith efforts shall be expended by Schering, as determined in its reasonable

 

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commercial judgement, based upon the facts and circumstances in existence and reasonably available to Schering at that time, and shall be exercised in a manner consistent with the discovery, development and commercialization of Schering’s other products of comparable commercial value, potential and stage of development. All of Schering’s diligence obligations hereunder are expressly conditioned upon the continuing absence of any adverse condition or event which warrants a delay in commercialization of an Agreement Product including, but not limited to, an adverse condition or event relating to the safety or efficacy of the Agreement Product or unfavorable pricing, pricing reimbursement, labeling or lack of Regulatory Approval, and Schering shall have no obligation to develop or market any such Agreement Product so long as in Schering’s opinion any such condition or event exists; provided that Schering shall use commercially reasonable efforts to overcome any unfavorable pricing or pricing reimbursement with respect to Agreement Products being commercialized under this Agreement. The Parties acknowledge and agree that none of the diligence obligations in this Section 3.5 shall apply to any Schering Compounds, the discovery, development and commercialization of which are the sole and exclusive responsibility of Schering.

ARTICLE IV

LICENSES AND EXCLUSIVITY

4.1 License to Schering .

4.1.1 License to Pharmacopeia Technology . Subject to the terms of Section 4.4.1, Pharmacopeia agrees to grant, and hereby grants to Schering an exclusive license under the Pharmacopeia Technology (exclusive even as to Pharmacopeia and its Affiliates) in the Territory, to make, have made, use, sell, offer to sell, import and export Agreement Products containing a Lead Compound which is a Hit or a corresponding Derivative Compound as an active ingredient. It is understood that such licenses shall include the right to conduct drug research and development, and the exclusive right to discover, develop, make, have made and use such Lead Compounds and corresponding Derivative Compounds, during the term of this Agreement.

4.1.2 License to Collaboration Technology . Pharmacopeia agrees to grant, and hereby grants to Schering an exclusive license under Pharmacopeia’s interest in the Collaboration Technology (exclusive even as to Pharmacopeia and its Affiliates), to make, have made, use, sell, offer to sell, import and export Agreement Products in the Territory. It is understood that such licenses shall include the right to conduct drug research and development, and the exclusive right to discover, develop, make, have made and use Agreement Compounds, during the term of this Agreement.

4.1.3 License to Collaboration Target-Specific Technology . Pharmacopeia agrees to grant, and hereby grants, to Schering an exclusive license (exclusive even as to Pharmacopeia and its Affiliates), under all of Pharmacopeia ’s interest in the Collaboration Target-Specific Technology for any and all purposes in the Territory, including the right to grant sublicenses.

4.1.4 *

4.2 Sublicenses . Schering shall have the right to sublicense the rights granted in Section 4.1 above. Each such sublicense shall be consistent with all the terms and conditions of this Agreement. Schering shall remain responsible to Pharmacopeia for all of each such Sublicensee’s applicable financial and other obligations due under this Agreement. Such Sublicensee shall not have the right to grant further sublicenses, and such sublicenses may not be assigned or transferred to any Third Party without the prior written consent of Pharmacopeia. Each sublicense shall provide for its continuation following early termination of the license rights of Schering hereunder and its assignment to Pharmacopeia. Promptly following the execution of each sublicense requiring Pharmacopeia’s consent hereunder, Schering shall give Pharmacopeia written notice of the existence and identity of each Sublicensee and identify the Agreement Product(s) sublicensed to such Sublicensee.

4.3 Direct Affiliate Licenses . Whenever Schering shall reasonably demonstrate to Pharmacopeia that, in order to facilitate direct royalty payments by an Affiliate, it is desirable that a separate license agreement be entered into between Pharmacopeia and such Affiliate, Pharmacopeia will grant such licenses directly to such Affiliate by means of an agreement which shall be consistent with all of the provisions hereof and Schering shall guarantee the Affiliate’s obligations thereunder and otherwise provide to Pharmacopeia assurances of performance satisfactory to Pharmacopeia. Schering shall reimburse Pharmacopeia for its reasonable attorneys’ fees and costs incurred in connection with any such separate license agreement.

 

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4.4 Third Party Rights .

4.4.1 Pharmacopeia Third Party Activities . It is understood that as of the Effective Date Pharmacopeia may have already granted, or on or after the Effective Date may grant, to Third Parties rights to acquire licenses for Pharmacopeia Compounds similar to Schering’s rights under this Article IV. Notwithstanding the licenses granted to Schering under Sections 4.1.1 and 4.1.4 above, it is possible that a Third Party already has or may acquire rights from Pharmacopeia with respect to one or more compounds of which Pharmacopeia is a sole or joint owner, which compounds were made and designed independently of Pharmacopeia’s activities in the Collaboration; accordingly, Pharmacopeia’s grant of rights under Sections 4.1.1 and 4.1.4 are limited to the extent that (i) a Third Party (either alone or jointly with Pharmacopeia) has filed a patent application with respect to such a compound prior to the filing by Schering (either alone or jointly with Pharmacopeia) of a patent application with respect to such a compound, or (ii) Pharmacopeia has previously granted a Third Party a license, an option to acquire a license, a right of first negotiation, field exclusivity, or a non-competition covenant with respect to such a compound, and are subject to any such grant of rights to a Third Party.

4.4.2 No Liability . It is understood and agreed that, even if Pharmacopeia complies with its obligations under this Agreement, compounds provided to Third Parties in the course of Pharmacopeia’s other business activities may result in Third Party patent applications and patents, including patent applications and patents owned by such Third Parties, or owned jointly by Pharmacopeia and such Third Parties, which could conflict with patent applications and patents owned by Schering, or jointly owned by Schering and Pharmacopeia hereunder. Pharmacopeia shall use reasonable efforts to avoid such conflict, which efforts shall be comparable to those used by Pharmacopeia in performing similar obligations under its agreements with Third Parties. It is understood that, unless Schering is damaged as a proximate result of a material breach by Pharmacopeia of any of the representations and warranties in Article VIII, then Pharmacopeia shall have no liability under this Agreement with respect to any such conflict.

4.4.3 Pharmacopeia Reports to Schering On Third Party Rights . During the period from the Effective Date until the First Commercial Sale of an Agreement Product, within thirty (30) days of a written demand by Schering concerning a Pharmacopeia license to a Third Party of a patent application owned or co-owned by Pharmacopeia, Pharmacopeia shall, to the extent it may do so without breaching any contractual or other legal obligation, provide Schering with a statement explaining why the invention(s) claimed in the patent application or technology licensed to such Third Party is independent of Pharmacopeia’s activities in the Collaboration. Such statement shall be supported by written records kept in the ordinary course of business consistent with pharmaceutical industry standards, provided that such records need not be provided to Schering at the time of providing such statement, but may have to be provided pursuant to Section 11.3. Such information shall be deemed Confidential Information of Pharmacopeia pursuant to this Agreement.

4.5 Collaboration Research Activities . Schering agrees to grant, and hereby grants, to Pharmacopeia a royalty-free, non-exclusive license under (i) Schering’s interest in the Collaboration Technology, and (ii) any Schering Technology which Schering, in its sole discretion, reasonably determines is necessary or useful for Pharmacopeia’s performance of the Collaboration, in each case to use during the term of the Collaboration and solely in performance of the Collaboration. Pharmacopeia will not be required to pay any fees to use such intellectual property, but will as a condition precedent to such use execute any consents or sublicenses required by any Schering licensor. Pharmacopeia shall not be required to execute any unreasonable consents or licenses and will not be in breach of this Agreement for failure to do so.

4.6 *

4.7 No Other Products . Neither Schering nor its Affiliates or Sublicensees shall commercialize any Hit, Lead Compound which is a Hit, Derivative Compound, Schering Derivative or other composition of matter claimed in a Collaboration Patent Right, other than as an Agreement Product in accordance with this Agreement.

 

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ARTICLE V

PAYMENTS

5.1 Payments By Schering . In partial consideration for Pharmacopeia’s conducting research activities in the Collaboration and the rights and licenses granted to Schering herein, Schering agrees to pay to Pharmacopeia the amounts set forth in Sections 5.2, 5.3, 5.4 and 5.5. *

5.2 Collaboration Funding .

5.2.1 Funding During Year One . Schering shall pay to Pharmacopeia research funding for the Collaboration at a rate of * per FTE per year during the first year of the Collaboration based upon the actual number of Pharmacopeia FTEs assigned to the Collaboration as set forth in Section 2.5.1, plus any additional FTEs (if any) agreed upon by the Parties under Section 2.3(i).

5.2.2 Funding During Subsequent Years . Schering shall pay to Pharmacopeia research funding for the Collaboration at an adjusted rate per FTE during the second year and each subsequent year of the Collaboration, based upon the actual number of Pharmacopeia FTEs assigned to the Collaboration in such year in accordance with Sections 2.5.2, 2.5.3 or 2.5.4 (as applicable), plus any additional FTEs (if any) agreed upon by the Parties under Section 2.3(i). The adjusted rate to be applied in each such year shall be *

5.2.3 Manner of Payment . As noted in Section 5.1, with respect to each Pharmacopeia FTE, * Research funding for the Collaboration under this Section 5.2 shall be payable quarterly in advance on the first day of each calendar quarter. Pharmacopeia shall send an invoice therefor to Schering fifteen (15) business days prior to the end of the preceding quarter, and Schering shall pay such invoiced amounts. It is understood that in the case of the first calendar quarter of the first year of the Collaboration, Pharmacopeia shall send an invoice to Schering as soon as practicable after the Effective Date. Each invoice will indicate the number of Pharmacopeia FTEs to be assigned to the Collaboration for such quarter and any adjustment from the prior quarter as determined in accordance with Section 5.2.4. Schering will use commercially reasonable efforts during each calendar year during the term of the Collaboration to pay its first calendar quarter Collaboration funding payments to Pharmacopeia on or before the first (1st) day of January; provided , however , that in the event Schering is unable to complete such payment, payment by Schering on or before the seventh (7th) day of January in such calendar year shall not constitute a breach or default by Schering.

5.2.4 Quarterly Adjustment . At the conclusion of each quarter, Pharmacopeia will calculate the actual number of FTEs provided by Pharmacopeia during that quarter and calculate any difference between the actual number of FTEs provided by Pharmacopeia and the number prepaid by Schering. Any overpayment or underpayment shall be reflected as a credit or additional charge, as the case may be, in the next quarterly invoice as per Section 5.2.3, and in the event that no further quarterly payments are due under this Section 5.2, then (i) any underpayment shall be paid by Schering to Pharmacopeia within fifteen (15) business days of receiving notice and invoice therefor, or (ii) Pharmacopeia shall within thirty (30) days reimburse Schering for any overpayment. For purposes of clarity and avoidance of doubt, the Parties acknowledge and agree that nothing in this Section 5.2.4 shall be construed as obligating Schering to pay for any Pharmacopeia FTEs actually working in the Collaboration during a given year of the Collaboration in excess of the number of FTEs specifically provided for in Section 2.2 during such year, unless such increased FTE support is agreed to in advance in writing by Schering.

5.3 Lead Compound Milestone . Schering shall pay to Pharmacopeia a milestone payment of * for each new Optimization Program initiated or agreed to by Schering with respect to a Screening Target based upon one or more Lead Compound(s) accepted by Schering in accordance with Section 2.8 that are Hits arising from Screening Programs conducted by Pharmacopeia. No such milestone shall be payable with respect to any Optimization Programs initiated or agreed to based upon Lead Compounds which are Schering Compounds. Such milestone payment shall be due within thirty (30) days after Schering notifies Pharmacopeia pursuant to Section 2.8.3 that it has accepted one or more Pharmacopeia Compounds as Lead Compounds. The milestone payment under this Section 5.3 shall only be payable * Further, it is understood and agreed that all amounts payable under this Section 5.3 are in addition to any milestone payments that may be due to Pharmacopeia under the corresponding provisions of the International Agreement. For the avoidance of doubt, it is understood and agreed that, for each new Optimization Program conducted by Pharmacopeia, Pharmacopeia shall be entitled to receive the milestone payment under this Section 5.3 and the milestone payment from Schering-Plough Ltd. under the corresponding provision of the International Agreement.

 

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5.4 Milestone Payments .

5.4.1 Events and Amounts .

(a) Milestones for Optimization Programs based upon Schering Compounds . Schering agrees to pay to Pharmacopeia the following amounts upon attainment, by or on behalf of Schering, its Affiliates or Sublicensees, of the indicated milestones with respect to any new Agreement Compounds/Agreement Products discovered by Pharmacopeia in performance of an Optimization Program based upon one or more Lead Compounds which are Schering Compounds (i.e., any Derivative Compounds resulting from such Optimization Program and/or any Schering Derivatives derived from such Derivative Compounds):

 

  (i) * upon nomination of a Development Candidate;

 

  (ii) *upon the filing and Acceptance of an IND or its equivalent;

 

  (iii) * upon initiation of treatment of the first patient in a Phase III clinical study;

 

  (iv) * upon filing and Acceptance of an NDA with the FDA; and

 

  (v) * upon Regulatory Approval in the Territory.

(b) Milestones for Optimization Programs based upon Hits . Schering agrees to pay to Pharmacopeia the following amounts upon attainment, by or on behalf of Schering, its Affiliates or Sublicensees, of the indicated milestones with respect to an Agreement Compound/Agreement Product arising from an Optimization Program based upon one or more Lead Compounds which are Hits, (i.e., any such Lead Compounds, related Hits, Derivative Compounds resulting from such Optimization Program and/or Schering Derivatives derived from such Lead Compounds, Hits or Derivative Compounds):

 

  (i) * upon nomination of a Development Candidate;

 

  (ii) * upon the filing and Acceptance of an IND or its equivalent;

 

  (iii) * upon initiation of treatment of the first patient in a Phase III clinical study;

 

  (iv) * upon filing and Acceptance of an NDA with the FDA; and

 

  (v) * upon Regulatory Approval in the Territory.

It is understood and agreed that all amounts payable under this Section 5.3.1 are in addition to any milestone payments that may be due to Pharmacopeia under the terms of the International Agreement.

5.4.2 Development Candidate . A Development Candidate shall have been deemed to have been nominated upon the earlier of the date (i) the Schering-Plough Research Institute Project Assessment Committee or its successor approves proceeding with full development of such compound, or (ii) Schering (or its Affiliate) initiates in vivo toxicology trials necessary, and meeting U.S. FDA (or corresponding European or Japanese) standards, for obtaining approval for use of such Agreement Compound in human clinical trials. Within thirty (30) days after the nomination of a Development Candidate, Schering shall notify Pharmacopeia thereof.

5.4.3 Manner of Payment . All payments made to Pharmacopeia by Schering pursuant to Section 5.4.1(a) or (b) shall be due within thirty (30) days after the achievement of the corresponding milestone and shall be nonrefundable and not creditable against other amounts due to Pharmacopeia. The payments provided for under this Section 5.4 shall only be payable once upon the first achievement of the indicated milestone with respect to an Agreement Compound and/or Agreement Product developed against a

 

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particular Target and no additional payments shall be due on subsequent or repeated achievement of the same milestone for another Agreement Compound and/or Agreement Product developed against the same Target. No milestones shall be payable under this Section 5.4 with respect to any compounds or products other than Agreement Compounds and Agreement Products, nor shall any payments be due under this Section 5.4 with respect to any Agreement Products discovered by Schering with respect to Targets which are not the subject of a Screening Program and/or Optimization Program, as provided in Section 2.11.

5.5 Royalties . In partial consideration for the know-how licenses, patent licenses and other rights granted to Schering hereunder, Schering shall pay royalties to Pharmacopeia based upon the sales of Agreement Products in the Territory. The parties acknowledge and agree that, except as expressly set forth herein, Schering’s obligation to pay such royalties is not conditioned upon the existence of patent protection for the Agreement Products.

5.5.1 Base Royalty . Schering shall pay to Pharmacopeia running royalties on Net Sales of Agreement Products by Schering, its Affiliates and Sublicensees in the Territory, as follows:

 

  (i) * of Net Sales of Agreement Products where the Agreement Compound in such Agreement Product is (1) a Lead Compound which is a Hit, or (2) a Derivative Compound discovered by Pharmacopeia in an Optimization Program based upon a Lead Compound which is a Hit, or (3) a corresponding Schering Derivative; or

 

  (ii) * of Net Sales of Agreement Products where the Agreement Compound in such Agreement Product is a Derivative Compound discovered by Pharmacopeia in an Optimization Program based upon a Lead Compound which is a Schering Compound;

 

  (iii) * of Net Sales of Agreement Products where the Agreement Compound in such Agreement Product is (1) a Lead Compound which is a Hit, or (2) a Derivative Compound, and in each case where such Agreement Product was developed and commercialized by Schering as a result of an independent screening program conducted by Schering pursuant to Section 2.11 against a Target which was not the subject of a Screening Program or Optimization Program under this Agreement; or

 

  (iv) * of net sales (to be determined in the same manner as Net Sales) of a pharmaceutical product containing as an active ingredient a Schering Derivative derived from a Derivative Compound discovered by Pharmacopeia in an Optimization Program based upon a Lead Compound which is a Schering Compound.

5.5.2 Royalty Term for Agreement Products . Schering’s obligation to pay royalties to Pharmacopeia under Sections 5.5.1(i), 5.5.1(ii), 5.5.1(iii) or 5.5.1(iv), as applicable, shall continue for each Agreement Product until the date which is the later of *

5.5.3 Single Royalty; Non-Royalty Sales . No royalty shall be payable under Section 5.5.1 above with respect to sales of Agreement Products among Schering, its Affiliates and Sublicensees for resale; however, a royalty shall be payable upon such resale by Schering’s Affiliates and Sublicensees to any Third Party. In no event shall more than one royalty be due hereunder with respect to any Agreement Product unit even if covered by more than one patent included in the Pharmacopeia Technology or Collaboration Technology. For purposes of clarity and avoidance of doubt, the Parties acknowledge and agree that under no circumstances will any royalty ever be payable under Sections 5.5.1(i) or 5.5.1(ii) with respect to sales of any Agreement Product resulting from an independent screening programs conducted by Schering pursuant to Section 2.11. No royalties shall accrue on the disposition of any Agreement Product in reasonable quantities by Schering, its Affiliates or its Sublicenses as (i) samples (promotional or otherwise), (ii) donations (for example, to non-profit institutions or government agencies for a non-commercial purpose), (iii) for use in clinical studies, or (iv) free of charge in compassionate use and/or indigent care programs.

 

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5.5.4 Third Party Royalties .

(a) Schering Responsibilities . Schering shall be responsible for the payment of any royalties due to licenses obtained from Third Parties relating to the manufacture, use, marketing, sale or distribution of Agreement Products by Schering, its Affiliates or Sublicensees under the Collaboration Technology or Schering Technology.

(b) Third Party Royalty Offset . Notwithstanding Section 5.5.4(a) above, if a Third Party alleges that the manufacture, use or sale of an Agreement Product infringes its patents, based solely on the practice of the Pharmacopeia Technology, Pharmacopeia and Schering shall consult regarding whether a license should be taken from such Third Party. If Pharmacopeia and Schering agree that such a license is required, Schering, its Affiliates or Sublicensees may, with respect to sales of such Agreement Product, pay royalties directly (or indirectly through Pharmacopeia) to the Third Party whose patents may be infringed by such sales. Schering may reduce any royalty due Pharmacopeia under Section 5.5.1 to reimburse Schering for any such royalties actually paid to Third Parties; provided that the amount of the reduction shall be equal to * of the royalty actually paid to such Third Parties with respect to sales of the Agreement Product in such country; provided , however , that in no event shall the royalty due Pharmacopeia for any calendar quarter, with respect to any such Agreement Product, be thereby reduced to * of the royalty due Pharmacopeia under Section 5.5.1 with respect to Net Sales in such country. If the Parties cannot promptly reach agreement they shall appoint an independent patent counsel reasonably acceptable to each of them to give an opinion, which will be binding as between the Parties, and the parties shall have no further recourse to dispute such opinion (including, without limitation, the provisions of Section 11.3, which shall not apply). If it is the independent patent counsel’s opinion that the patent is valid and infringed by the sale of such Agreement Product due to use of the Pharmacopeia Technology, Schering may settle the matter in its sole discretion on such terms as it deems appropriate, provided that such settlement does not contain an admission or acknowledgment of infringement or invalidity.

5.5.5 Compulsory Royalty Reductions . If the royalties set forth herein are higher than the maximum royalties permitted by the law or regulation in any country or territory or possession thereof in the world, the royalty payable for sales in such country, territory or possession shall be equal to the maximum permitted royalty under such law or regulations.

5.5.6 Royalty Overpayment . In the event Schering pays Pharmacopeia royalties in excess of the amounts due under Section 5.5.1 herein, Schering shall promptly notify Pharmacopeia providing a written explanation of the amount of overpayment. Any such overpayment shall be fully creditable against royalties subsequently due hereunder.

5.6 Reports; Payment of Royalty; Payment Exchange Rate and Currency Conversions .

5.6.1 Royalty Reports and Payments . After the First Commercial Sale of an Agreement Product on which royalties are payable by Schering, its Affiliate or Sublicensees hereunder, Schering shall make quarterly written reports to Pharmacopeia within sixty (60) days after the end of each calendar quarter, stating in each such report separately for Schering and each of its Affiliates and Sublicensees the number, description, and aggregate Net Sales by country of each Agreement Product sold during the calendar quarter upon which a royalty is payable under Section 5.5 above. Subject to any reductions permitted pursuant to the express terms of this Agreement, concurrently with the making of such reports, Schering shall pay to Pharmacopeia royalties at the rates specified in Section 5.5.1.

5.6.2 Payment Method . All payments due under this Agreement shall be made by bank wire transfer in immediately available funds to an account designated by Pharmacopeia. All payments hereunder shall be made in U.S. dollars. Any payments that are not paid on the date such payments are due under this Agreement shall bear interest, calculated on the number of days such payment is delinquent, at the lesser of: (i) the prime rate as reported by the Chase Manhattan Bank, New York, New York, on the date such payment is due, plus an additional two percent (2%), or (ii) the maximum rate permitted by applicable law.

5.6.3 Place of Royalty Payment and Currency Conversions . Royalties shall be deemed payable by the entity making the Net Sales from the country in which earned in local currency and subject to foreign exchange regulations then prevailing. Royalty payments shall be made in United States dollars to the extent that free conversion to United States dollars is permitted. The rate of

 

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exchange to be used in any such conversion from the currency in the country where such Net Sales occurs shall be in accordance with the policy set forth in Exhibit A hereto. If, due to restrictions or prohibitions imposed by national or international authority, payments cannot be made as aforesaid, the Parties shall consult with a view to finding a prompt and acceptable solution, and Schering or its designated Affiliates will, from time to time, deal with such monies as Pharmacopeia may lawfully direct at no additional out-of-pocket expense to Schering. Notwithstanding the foregoing, if royalties in any country cannot be remitted to Pharmacopeia for any reason within six (6) months after the end of the calendar quarter during which they are earned, then Schering shall be obligated to deposit the royalties in a bank account in such country in the name of Pharmacopeia.

5.7 Maintenance of Records; Audits .

5.7.1 Records; Inspection . Schering and its Affiliates shall keep complete, true and accurate books of account and records for the purpose of determining the royalty amounts payable under this Agreement, which books and records shall be maintained in accordance with Schering’s records retention policies. Upon prior written notice from Pharmacopeia, Schering shall, within a period not to exceed forty-five (45) days, permit an independent certified public accounting firm of nationally recognized standing selected by Pharmacopeia and reasonably acceptable to Schering, at Pharmacopeia’s expense, to have access during normal business hours to examine pertinent books and records of Schering and/or its Affiliates as may be reasonably necessary to verify the accuracy of the royalty reports hereunder. The examination shall be limited to pertinent books and records for any calendar year ending not more than thirty-six (36) months prior to the date of such request. Such inspections may be made no more than once each calendar year. In the event that the accounting firm correctly concludes that a variation or error has occurred resulting in an underpayment of royalties by Schering of five percent (5)% or more of the amount actually due for the period covered by the inspection, Schering shall pay to Pharmacopeia such additional amounts, as well as the costs relating to the inspection, within thirty (30) days of receipt of an invoice for such amounts. Any overpayment of royalties by Schering discovered through such audit shall be fully creditable against royalties subsequently due hereunder. Schering may designate competitively sensitive information which such auditor may not disclose to Pharmacopeia; provided , however , that such designation shall not encompass the auditor’s conclusions. The accounting firm shall disclose to Pharmacopeia only whether the royalty reports are correct or incorrect and the specific details concerning any discrepancies. No other information shall be provided to Pharmacopeia. The accounting firm employees shall sign confidentiality agreements acceptable to Schering as a condition precedent to their inspection. Schering shall include in each sublicense granted by it pursuant to this Agreement a provision requiring the Sublicensee to make reports to Schering, to keep and maintain records of sales made pursuant to such sublicense and to grant access to such records by Pharmacopeia’s independent accountant to the same extent required of Schering under this Agreement. Upon expiration of the thirty-six (36) month period immediately following the receipt by Pharmacopeia of Schering’s fourth quarter royalty report for a given calendar year in accordance with Section 5.6.1, the calculation of royalties payable with respect to such year shall be binding and conclusive upon Pharmacopeia, and Schering, its Affiliates and its Sublicensees shall be released from any liability or accountability with respect to royalties for such year, except for instances of fraud or other intentional misconduct by Schering.

5.8 Coordination With Payments under International Agreement . The milestones and royalties payable by Schering under Sections 5.3, 5.4 and 5.5 are in consideration for the rights and licenses granted to Schering under this Agreement and are in addition to any amounts payable to Pharmacopeia under the International Agreement. It is understood and agreed that, with respect to the specific milestones payable under Sections 5.4.1(a)(i)-(iii) and 5.4.1(b)(i)-(iii), the occurrence of the same milestone event will result in milestone payment obligations under both this Agreement and the corresponding provisions of the International Agreement. However, the specific milestones payable under Sections 5.4.1(a)(iv) and (v) and Sections 5.4.1(b)(iv) and (v) under this Agreement and the analogous milestones under the International Agreement shall be paid, respectively, upon occurrence of the relevant milestone event specified in this Agreement or the International Agreement.

5.9 Tax Matters .

5.9.1 Withholding Taxes . All royalty amounts required to be paid to Pharmacopeia pursuant to this Agreement shall be paid with deduction for withholding for or on account of any taxes (other than taxes imposed on or measured by net income) or similar governmental charge imposed by a jurisdiction other than the United States (“Withholding Taxes”) to the extent Pharmacopeia and/or its Affiliates or their successors has the lawful rights to utilize the Withholding Taxes paid by Schering as a

 

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credit against Pharmacopeia’s and/or its Affiliates regular U.S. tax liability. Schering shall provide Pharmacopeia documentation evidencing payment of any Withholding Taxes hereunder in a manner that is satisfactory for purposes of the U.S. Internal Revenue Service. Any Withholding Taxes paid when due hereunder shall be for the account of Pharmacopeia and shall not be included in the calculation of Net Sales. Payments of Withholding Taxes made by Schering pursuant to this Section 5.9.1 shall be made based upon financial information provided to Schering by Pharmacopeia, and to the extent that such information is incorrect Pharmacopeia shall be liable for any deficiency, and any fine, assessment or penalty imposed by any taxing authority in the Territory for any deficiency in the amount of any such Withholding Taxes, or the failure to make payment of Withholding Taxes, based upon such incorrect information. If Schering is required to pay any such deficiency, or any fine, assessment or penalty for any such deficiency based upon such incorrect information (except to the extent caused by Schering’s gross negligence or willful misconduct), Pharmacopeia shall promptly reimburse Schering for such payments, which shall not be included in the calculation of Net Sales.

5.10 Product Development Costs . Schering shall, at Schering’s expense, be responsible for conducting all development of Agreement Compounds, Agreement Products, Schering Compounds, and all commercialization of Agreement Products.

ARTICLE VI

PATENTS AND INVENTIONS

6.1 Ownership of Schering Technology and Pharmacopeia Technology . It is understood and agreed that (i) Schering shall own all Schering Technology including, without limitation, Schering Improvements, and (ii) Pharmacopeia shall own all Pharmacopeia Technology including, without limitation, Pharmacopeia Improvements.

6.2 Ownership of Collaboration Technology . The Parties anticipate that the Collaboration may result in new inventions, discoveries and innovations, as well as improvements to existing technologies, whether patentable or not, within the Collaboration Technology. Ownership of Collaboration Technology shall be determined based upon U.S.

Patent Laws and the following guidelines; provided , however , that ownership rights to all Collaboration Technology shall be subject to the applicable licenses and other rights granted under Article IV of this Agreement.

(a) Inventions by Schering Employees . Title to all Collaboration Technology invented solely by employees of Schering working on the Collaboration at Pharmacopeia, together with any Derivative Compounds synthesized by Pharmacopeia pursuant to Section 2.9, shall be deemed to be owned by Schering.

(b) Inventions by Pharmacopeia Employees . Title to all Collaboration Technology invented solely by employees of Pharmacopeia shall be deemed to be owned by Pharmacopeia.

(c) Joint Inventions . Title to all Collaboration Technology invented jointly by one or more employees of Schering working on the Collaboration at Pharmacopeia, and one or more employees of Pharmacopeia shall be deemed to be jointly owned by Schering and Pharmacopeia.

6.3 Filing, Prosecution and Maintenance of Patents .

6.3.1 Collaboration Technology . Schering shall have the right to prepare, file, prosecute and maintain in such countries as it deems appropriate in its discretion, at its own expense and upon appropriate consultation with Pharmacopeia, patent applications and patents, and to conduct any interferences, re-examinations, reissues, oppositions or requests for patent term extension or governmental equivalents thereto within the Collaboration Technology, and Pharmacopeia shall give reasonable cooperation in connection therewith, at Schering’s request and expense. Schering shall provide Pharmacopeia with copies of any new patent applications claiming Collaboration Technology which are proposed to be filed by Schering, as provided in Section 6.4.1. In the event that Schering does not file a patent or patent application claiming an invention within such Collaboration Technology, or if it ceases

 

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to so prosecute, maintain, conduct any interferences, re-examinations, reissues, oppositions or requests for patent term extension or governmental equivalents thereto relating to such an invention, Pharmacopeia shall have the right, in its sole discretion, to undertake such activities at its own expense, and Schering shall give reasonable cooperation in connection therewith, at Pharmacopeia’s expense.

6.3.2 Schering Technology . Schering shall have the right to prepare, file, prosecute and maintain in such countries as it deems appropriate in its discretion, at its own expense, patent applications and patents, and to conduct any interferences, re-examinations, reissues, oppositions or requests for patent term extension or governmental equivalents thereto within the Schering Technology and Pharmacopeia shall give reasonable cooperation in connection therewith, at Schering’s request and expense.

6.3.3 Pharmacopeia Technology . Pharmacopeia shall have the right to prepare, file, prosecute and maintain in such countries as it deems appropriate in its discretion, at its own expense, patent applications and patents, and to conduct any interferences, re-examinations, reissues, oppositions or requests for patent term extension or governmental equivalents thereto within the Pharmacopeia Technology, and Schering shall give reasonable cooperation in connection therewith, at Pharmacopeia’s request and expense.

6.4 Cooperation .

6.4.1 Cooperation . Upon request, and at the requesting Party ’s expense, each of Pharmacopeia and Schering shall provide the other Party reasonable assistance to prepare, file, prosecute and maintain patents and patent applications covering any Collaboration Technology, Schering Improvements or Pharmacopeia Improvements which the requesting Party has the right to file. Reasonable assistance shall include, without limitation, providing the requesting Party with necessary or useful data and information relating to the Collaboration Technology, Schering Improvements or Pharmacopeia Improvements, as the case may be, and reasonable access to the inventors of said inventions, as well as causing the execution of required patent assignments and/or other documents. With respect to all patent applications claiming Collaboration Technology, or any Derivative Compounds, Lead Compounds which are Hits, or Schering Derivatives, the filing Party shall give the non-filing Party an opportunity to review the text of such patent applications before filing, shall consult with the non-filing Party with respect thereto, and shall supply the non-filing Party with a copy of the applications as filed, together with notice of its filing date and serial number. Schering will identify to Pharmacopeia any of Schering’s proprietary information contained in such documents to be provided to Pharmacopeia to ensure that Pharmacopeia will protect Schering’s proprietary information, including without limitation, information relating to Targets. In addition, with respect to applications which do not include Pharmacopeia inventors, Schering may redact or provide in coded form any information contained in such documents to be provided to Pharmacopeia to the extent necessary (in Schering’s opinion) to protect Schering’s proprietary information, including without limitation, information relating to Targets. Pharmacopeia and Schering shall each keep the other Party advised of the status of the actual and prospective patents and patent applications within the Collaboration Patent Rights for which it is responsible, and upon the written request of the other Party, will provide advance copies of any substantive papers related to the filing, prosecution and maintenance of such Collaboration Patent Rights.

6.5 Enforcement .

6.5.1 Notice . Each Party shall promptly notify the other of its knowledge of any actual or potential infringement of the Collaboration Technology by a Third Party.

6.5.2 Collaboration Technology . Schering shall have the initial right, but not the obligation, to take reasonable legal action to enforce against infringements by Third Parties or defend any declaratory judgment action relating to any patent within the Collaboration Technology at its sole cost and expense. If, within six (6) months following receipt of notice of such infringement from Pharmacopeia (or written notice of a declaratory judgment action alleging invalidity or unenforceability of such Collaboration Technology), Schering does not take such action against a commercially significant infringement, Pharmacopeia shall, in its sole discretion, have the right, but not the obligation to take such action at its sole expense.

6.5.3 Schering Technology and Pharmacopeia Technology . It is understood and agreed that Pharmacopeia shall have the sole right, but not the obligation, to initiate and conduct legal proceedings to enforce the Pharmacopeia Technology against any actual

 

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or threatened infringement or misappropriation or defend any declaratory judgment action relating thereto, at its sole expense, and that Schering shall have the sole right, but not the obligation, to initiate and conduct legal proceedings to enforce the Schering Technology against any actual or threatened infringement or misappropriation or defend any declaratory judgment action relating thereto, at its sole expense.

6.5.4 Cooperation; Costs and Recoveries . Each Party agrees to render such reasonable assistance as the enforcing Party may request, and at the enforcing Party’s expense. Costs of maintaining any such action shall be paid by the Party bringing the action and any damages or settlements recovered therefrom shall belong to such Party. To the extent that Schering recovers any lost profits or other recovery based upon Third Party sales of infringing products, Pharmacopeia shall receive an equitable share of such recovery, as determined based upon the royalties Pharmacopeia would have been entitled to under this Agreement on Net Sales by Schering, its Affiliates or Sublicensees of the relevant Agreement Products corresponding to such lost profits. If Schering, in its sole discretion, agrees to settle any such infringement action by granting a sublicense to the Third Party infringer, and such Third Party, but for the grant of such sublicense, would be infringing a claim of an issued patent in the Collaboration Technology, or a composition-of-matter claim of an issued patent in the Schering Technology, Schering shall be entitled to receive all consideration payable by such Third Party for the grant of the license; provided , however , that net sales of such Third Party products in the Territory on which Schering receives such consideration (including, without limitation, running royalties or lump sum payments) shall be treated as Net Sales for purposes of this Agreement, and further provided that, notwithstanding anything herein to the contrary, Schering’s royalty obligations to Pharmacopeia with respect to such Third Party sales in any calendar quarter shall not exceed fifty percent (50%) of the royalties received by Schering from such Third Party for the same quarter.

6.6 Infringement Claims . If the manufacture, sale or use of any Agreement Product pursuant to this Agreement because of the practice of the Pharmacopeia Technology, Collaboration Technology or Schering Technology, results in any claim, suit or proceeding alleging patent infringement against Pharmacopeia or Schering (or their respective Affiliates or Sublicensees), such Party shall promptly notify the other Party hereto in writing setting forth the facts of such claim in reasonable detail. The Party subject to such claim shall have the exclusive right and obligation to defend and control the defense of any such claim, suit or proceeding, at its own expense, using counsel of its own choice; provided , however , it shall not enter into any settlement which admits or concedes that any aspect of (i) the Schering Technology or Collaboration Technology in the case of Pharmacopeia, and (ii) the Pharmacopeia Technology or Collaboration Technology in the case of Schering, is invalid or unenforceable without the prior written consent of such other Party. The Party subject to the claim shall keep the other Party hereto reasonably informed of all material developments in connection with any such claim, suit or proceeding.

6.7 Certification under Drug Price Competition and Patent Restoration Act . Pharmacopeia and Schering each shall immediately give written notice to the other of any certification of which they become aware filed pursuant to 21 U.S.C.§§355(b)(2)(A)(iv) and 355(j)(2)(A)(vii) claiming that Collaboration Patent Rights do not cover the use or sale of any product(s) equivalent to an existing Agreement Product(s) by a Third Party. Schering shall have the right to bring an infringement action, in its sole discretion and at its own expense, in its own name and/or in the name of Pharmacopeia, subject to Section 6.5 above. The provisions of Section 6.5.4 shall apply to any such infringement action.

6.8 Patent Term Restoration . The Parties hereto shall give reasonable cooperation to each other in obtaining patent term restoration or supplemental protection certificates or their equivalents in any country in the Territory where applicable to the Collaboration Technology.

ARTICLE VII

CONFIDENTIALITY

7.1 Confidential Information . Except as expressly provided herein, the Parties agree that, * the receiving Party shall not disclose and except as expressly provided in this Article 7, shall not use for any purpose any confidential information (“Confidential Information”) furnished to it by the disclosing Party hereto pursuant to this Agreement except to the extent that it can be established by the receiving Party by competent proof that such information:

(i) was already known to the receiving Party, other than under an obligation of confidentiality, at the time of disclosure;

 

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(ii) was generally available to the public or otherwise part of the public domain at the time of its disclosure to the receiving Party;

(iii) became generally available to the public or otherwise part of the public domain after its disclosure and other than through any act or omission of the receiving Party in breach of this Agreement;

(iv) was independently developed by the receiving Party as demonstrated by documented evidence prepared contemporaneously with such independent development; or

(v) was subsequently lawfully disclosed to the receiving Party, other than under a duty of confidentiality, by a Third Party that had the right to make such disclosure.

7.2 Permitted Use and Disclosures . Each Party hereto may use or disclose Confidential Information disclosed to it by the other Party to the extent such information is included in the Pharmacopeia Technology, Schering Technology or Collaboration Technology, as the case may be, and to the extent (i) such use or disclosure is reasonably necessary and permitted in the exercise of the rights granted hereunder in filing or prosecuting patent applications, prosecuting or defending litigation, (ii) such disclosure is reasonably required to be made to any institutional review board of any entity conducting clinical trials with Agreement Compound(s) and/or Agreement Product(s), or to any governmental or other regulatory agency, in order to gain approval to conduct clinical trials or to market Agreement Compound(s) and/or Agreement Products, (iii) such disclosure is required by law, regulation, rule, act or order of any governmental authority, court, or agency, or is made in connection with submitting required information to tax or other governmental authorities, or (iv) such disclosure or use is reasonably required in conducting clinical trials, or making a permitted sublicense or otherwise exercising license rights expressly granted to it by the other Party pursuant to the terms of this Agreement; in each case, provided that if a Party is required to make any such disclosure of another Party’s Confidential Information, other than pursuant to a confidentiality agreement, it will give reasonable advance notice to the other Party of such disclosure and, save to the extent inappropriate in the case of patent applications, will use its reasonable diligent efforts to secure confidential treatment of such Confidential Information in consultation with the other Party prior to its disclosure (whether through protective orders or otherwise) and disclose only the minimum necessary to comply with such requirements.

7.3 Return of Confidential Information . Following termination of this Agreement, at any time upon request of the disclosing Party, the receiving Party will return all documents, and copies thereof, containing the disclosing Party ’s Confidential Information that are still in the receiving Party’s possession or control; however, the receiving Party may retain one copy of such documents in a secure location solely for the purpose of determining its obligations hereunder, to comply with any applicable regulatory requirements, or to defend against any product liability claims.

7.4 Nondisclosure of Terms . Each of the Parties hereto agrees not to disclose to any Third Party the existence or the terms of this Agreement without the prior written consent of each other Party hereto, except to such Party’s attorneys, advisors, investors and others on a need to know basis under circumstances that reasonably ensure the confidentiality thereof, or to the extent required by law. Notwithstanding the foregoing, the Parties will agree upon a press release to announce the effectiveness of this Agreement, together with a corresponding Q&A outline for use in responding to inquiries about the Agreement; and in such event, Pharmacopeia and Schering may each disclose to Third Parties the information contained in such press release and Q&A without the need for further approval by the other. In addition, Pharmacopeia may make public statements regarding progress with respect to the development and commercialization of Agreement Compounds and/or Agreement Products, including announcement of the achievement of milestones, following consultation with Schering and with the written consent of Schering. Nothing in this Section 7.4 shall prohibit a Party from making such disclosures to the extent reasonably required under applicable federal or state securities laws or any rule or regulation of any nationally recognized securities exchange. In such event, however, the disclosing Party shall use good faith efforts to notify and consult with the other Party prior to such disclosure and, where applicable, shall diligently seek confidential treatment to the extent available.

 

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7.5 Publication . Any manuscript by Schering or Pharmacopeia or their Affiliates describing Agreement Products shall be subject to the prior review of the other Party at least ninety (90) days prior to submission. Further, to avoid loss of patent rights as a result of premature public disclosure of patentable information, the receiving Party shall notify the disclosing Party in writing within thirty (30) days after receipt of a disclosure whether the receiving Party desires to file a patent application on any invention disclosed in such scientific results. In the event that the receiving Party desires to file such a patent application, the disclosing Party shall withhold publication or disclosure of such scientific results until the earlier of (i) a patent application is filed thereon, or (ii) the Parties determine after consultation that no patentable invention exists, or (iii) one hundred and eighty (180) days after receipt by the disclosing Party of the receiving Party’s written notice of the receiving Party’s desire to file such patent application, or such other period as is reasonable for seeking patent protection. Further, if such scientific results contain the information of the receiving Party that is subject to use and nondisclosure restrictions under this Article 7, the disclosing Party agrees to remove such information from the proposed publication or disclosure.

7.6 Pharmacopeia Employees . All Pharmacopeia employees assigned to work exclusively on Collaboration research projects pursuant to Section 2.5, shall be required to have read and understood the Collaboration Business Conduct Policy. Any Pharmacopeia employees assigned to work exclusively on Collaboration research projects shall also be subject to non-compete obligations, as set forth below, with respect to any Target with respect to which Collaboration research efforts directed to such Target are performed at Pharmacopeia (including, without limitation, the design and synthesis of Derivative Compounds based on Lead Compounds). None of the individual Pharmacopeia chemists participating in Target specific collaboration research shall * Pharmacopeia shall be liable for any breach of the Collaboration Business Conduct Policy and/or these non-compete obligations by its employees. *, Pharmacopeia shall use reasonably diligent efforts to ensure that its employees working on the Collaboration do not disclose or provide access to any Collaboration Target-Specific Technology, Schering Technology, or the results of any screening or other Target specific research performed at Pharmacopeia in the Collaboration, to any Pharmacopeia employees not working on the Collaboration (except to the extent reasonably necessary for Pharmacopeia to ensure its compliance with its exclusivity obligations hereunder) or to any Third Parties.

ARTICLE VIII

REPRESENTATIONS, WARRANTIES AND COVENANTS

8.1 Schering . Schering warrants, represents and covenants on behalf of itself and its Affiliates that: (i) it has the legal right and power to extend the rights granted in this Agreement; (ii) it has the legal power, authority and right to enter into this Agreement, and to perform all its obligations hereunder, and (iii) it has not previously granted, and during the term of this Agreement will not knowingly make any commitment or grant any rights which in any material way conflict with the rights and licenses granted herein.

8.2 Pharmacopeia . Pharmacopeia represents, warrants and covenants on behalf of itself and its Affiliates that: (i) it has the legal right and power to extend the rights granted in this Agreement; (ii) it has the legal power, authority and right to enter into this Agreement, and to perform all its obligations hereunder; (iii) it has not previously granted, and during the term of this Agreement will not knowingly make any commitment or grant any rights which in any material way conflict with the rights and licenses granted herein; (iv) to the best of its knowledge as of the Effective Date, there are no existing or threatened actions, suits or claims pending against it with respect to the Pharmacopeia Technology; (v) to the best of its knowledge as of the Effective Date, it is not aware of any Existing Pharmacopeia Know-How which is not available for use for all purposes contemplated by this Agreement; and (vi) to the best of its knowledge as of the Effective Date, it owns or controls all of the Pharmacopeia Technology, and has the rights to grant the licenses or sublicenses granted to Schering hereunder with respect thereto.

8.3 Compliance with Agreement and Laws . Each Party shall comply in all material respects with the terms of this Agreement and with all laws, rules and regulations applicable to the discovery, development, manufacture, distribution, import and export and sale of pharmaceutical products pursuant to this Agreement.

 

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8.4 Disclaimer . Schering and Pharmacopeia expressly disclaim any representation, warranty or guaranty that the Collaboration will be successful. EXCEPT AS OTHERWISE EXPRESSLY SET FORTH IN THIS AGREEMENT, PHARMACOPEIA AND SCHERING AND THEIR RESPECTIVE AFFILIATES MAKE NO REPRESENTATIONS AND EXTEND NO WARRANTIES OR CONDITIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED, WITH RESPECT TO THE PHARMACOPEIA TECHNOLOGY, THE SCHERING TECHNOLOGY, THE COLLABORATION TECHNOLOGY, LEAD COMPOUNDS, DERIVATIVE COMPOUNDS, AGREEMENT COMPOUNDS OR AGREEMENT PRODUCTS, OR INFORMATION DISCLOSED PURSUANT TO ARTICLE VII, AND EXPRESSLY DISCLAIM ALL WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, VALIDITY OF THE PHARMACOPEIA TECHNOLOGY, COLLABORATION TECHNOLOGY OR SCHERING TECHNOLOGY (IN EACH CASE, WHETHER PATENTED OR UNPATENTED), OR NONINFRINGEMENT OF THE INTELLECTUAL PROPERTY RIGHTS OF THIRD PARTIES.

ARTICLE IX

INDEMNIFICATION

9.1 Indemnification by Schering . Schering shall indemnify, defend and hold harmless Pharmacopeia and its Affiliates, and each of its and their respective employees, officers, directors and agents (the “Pharmacopeia Indemnitees”) from and against any and all liability, loss, claims, damage, cost, and expense (including reasonable attorneys ’ and professionals’ fees and other expenses of litigation) (collectively, a “Liability”) arising out of or in connection with Third Party claims relating to (i) the discovery, development, manufacture, use, testing, marketing, sale or other disposition of Agreement Products by or on behalf of Schering or its Affiliates or Sublicensees, (ii) performance of the Collaboration by Schering, (iii) any injury, illness or disease suffered by any Schering employees in connection with the performance of the Collaboration, (iv) the use of any and all Targets with respect to which research activities are conducted in the Collaboration, including without limitation claims in connection with materials relating to such Target, or (v) any breach by Schering of its representations and warranties made under this Agreement, except, in each case, to the extent such Liabilities result from the gross negligence or willful misconduct of Pharmacopeia, its Affiliates, or any of their respective employees, officers, directors or agents.

9.2 Indemnification by Pharmacopeia . Pharmacopeia shall indemnify, defend and hold harmless Schering and its Affiliates, and each of its and their respective employees, officers, directors and agents (the “Schering Indemnitees”) from and against any Liability (as defined above) arising out of or in connection with Third Party claims relating to (i) the performance of the Collaboration by Pharmacopeia except to the extent directly related to the use of Targets, (ii) any injury, illness or disease suffered by any Pharmacopeia employees in connection with the performance of the Collaboration, (iii) any product based upon a Pharmacopeia Compound developed, manufactured, used, sold or otherwise distributed by or on behalf of Pharmacopeia, its Affiliates or Licensees, as permitted under this Agreement (including, without limitation, product liability and patent infringement claims), (iv) any breach of Pharmacopeia’s contractual obligations to Third Parties, or (v) any breach by Pharmacopeia of its representations and warranties made under this Agreement, except, in each case, to the extent such Liabilities result from the gross negligence or willful misconduct of Schering, its Affiliates, or any of their respective employees, officers, directors or agents.

9.3 No Consequential Damages . Except with respect to Third Party claims as provided for under Sections 9.1 and 9.2, in no event shall any Party to this Agreement have any claims against or liability to the other Party for any special, consequential or incidental damages arising under this Agreement under any theory of liability.

9.4 Procedure . In the event that any Indemnitee intends to claim indemnification under this Article IX, it shall promptly notify the other Party in writing of any such alleged Liability. The indemnifying Party shall have the right to control the defense thereof with counsel of its choice; provided , however , that any Indemnitee shall have the right to retain its own counsel, with the fees and expenses to be paid by the indemnifying Party, if representation of such Indemnitee by the counsel retained by the indemnifying Party would be inappropriate due to actual or potential differing interests between such Indemnitee and any other Party represented by such counsel in such proceeding. The affected Indemnitees shall cooperate reasonably with the indemnifying Party and its legal representatives in the investigation and defense of any action, claim or liability covered by this Article IX. Neither Party may settle a claim or action related to a Liability for which it or the other Party seeks indemnification hereunder without the consent of the other Party, if such settlement would impose any monetary obligation on the other Party or require the other Party to submit to an injunction or otherwise limit the other Party ’s rights under this Agreement. Any payment made by a Party to settle any such claim or action shall be at its own cost and expense.

 

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9.5 Insurance . Each Party shall obtain and maintain throughout the term of this Agreement statutory Workers’ Compensation and Employer’s Liability insurance covering all employees engaged in the performance of work under this Agreement. Each Party shall provide the other Party with evidence of such insurance and/or self-insurance program, upon request.

ARTICLE X

TERM AND TERMINATION

10.1 Term and Expiration . This Agreement shall be effective as of the Effective Date and unless terminated earlier as provided in this Article X or by mutual written agreement of the Parties, the term of this Agreement shall continue in full force and effect, on a country-by-country and product-by-product basis, until Schering and its Affiliates and Sublicensees have no further obligation to pay royalties under Article V hereof in a country, at which time the Agreement shall expire in its entirety in such country and the Parties shall have no further payment obligations or other financial obligations to each other with respect to the continuing use in such country of Pharmacopeia Technology, Schering Technology and/or Collaboration Technology, as the case may be, in the manner licensed herein. As royalty payment obligations for an Agreement Product expire in a country, even if the Agreement thereafter remains in effect in such country, Schering, its Affiliates and Sublicensees, shall no longer have any remaining payment obligations hereunder with respect to such Agreement Product in that country.

10.2 Termination for Cause . This Agreement may be terminated by written notice by either Party at any time during the term of this Agreement if the other Party (the “Breaching Party”) is in material breach or default of any of its material obligations hereunder (including, without limitation, any payment obligations), as follows: (i) the terminating Party shall send written notice of the breach or default to the Breaching Party; and (ii) if such default or breach thereafter continues for sixty (60) days after written notice thereof was provided to the Breaching Party, then the termination shall become effective at the end of such sixty (60) day period, unless the Breaching Party (or any other party on its behalf) has cured any such breach or default prior to the expiration of the sixty (60) day period or has commenced activities reasonably expected to cure such breach within such sixty (60) day period and thereafter uses diligent efforts to complete the cure as soon as practicable.

10.3 Termination Upon Bankruptcy or Insolvency . This Agreement may be terminated by Pharmacopeia giving written notice of termination to Schering upon the filing of bankruptcy or insolvency of Schering or the appointment of a receiver for the assets of Schering, or the making by Schering of an assignment for the benefit of creditors, or the institution of any proceedings against Schering under any bankruptcy law. Termination shall be effective upon the date specified in such notice. The rights of Schering under this Agreement shall not terminate in the event of a bankruptcy of Pharmacopeia, unless Schering elects to terminate this Agreement in accordance with the following provisions of this Section 10.3. In the event that (i) Pharmacopeia shall make an assignment for the benefit of creditors, file a petition in bankruptcy, petition or apply to any tribunal for the appointment of custodian, receiver or any trustee for it or a substantial part of its assets, or shall commence any case or proceeding under any bankruptcy, reorganization, arrangement, readjustment of debt, dissolution or liquidation law or statute of any jurisdiction, whether now or hereafter in effect; or (ii) if there shall have been filed any such bona fide petition or application, or any such proceeding shall have been commenced against it, in which an order for relief is entered or which remains undismissed for a period of sixty (60) days or more; or (iii) if Pharmacopeia by any act or omission of act shall indicate its consent to, approval of or acquiescence in any such bona fide petition, application, or proceeding or order for relief or the appointment of a custodian, receiver or trustee for it or any substantial part of its property, or shall suffer any such custodianship, receivership or trusteeship to continue undischarged for a period of sixty (60) days or more (each such event a “Pharmacopeia Bankruptcy Event”), then Schering shall have the following rights. Schering shall have the right, in its sole discretion, to elect to terminate this Agreement by giving written notice of such termination to Pharmacopeia. In the event that Schering does not elect to terminate this Agreement, then notwithstanding any rejection of this Agreement by Pharmacopeia (which, for purposes of this Section 10.3, includes any debtor in possession, trustee or other entity that may succeed Pharmacopeia) pursuant to 11 U.S.C. §365, Schering shall retain all of its rights, benefits, licenses, protections and privileges under this Agreement and shall be entitled to all of the rights, benefits and protections of a licensee under 11 U.S.C. 365(n). Schering will have the right (including, without limitation, the right and ability to cure any and all defaults by

 

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Pharmacopeia under this Agreement, any agreement supplementary hereto, and any agreement with a Third Party affecting or comprising all or a part of the Pharmacopeia Technology, and to take any other actions, to oppose a rejection pursuant to 11 U.S.C. §365 of this Agreement, and to contract directly with Third Parties, if any, involved in contracted arrangements with Pharmacopeia with respect to performance of the Collaboration), provided that Schering’s obligations to make payments to Pharmacopeia under this Agreement shall automatically be reduced by the amount of all out-of-pocket costs and expenses incurred by Schering in exercising such rights. The Parties acknowledge and agree that all information, data and other intellectual property referred to in this Section 10.3 (including, without limitation, Pharmacopeia Technology) and all Agreement Compounds, Agreement Products, Collaboration Technology and any other intellectual property that is licensed, or is the subject of any other right, benefit, protection or privilege that is granted, transferred or otherwise afforded, to Schering hereunder is “intellectual property” within the meaning of 11 U.S.C. §365.

10.4 Termination for Pharmacopeia Change in Control .

10.4.1 Termination of Entire Agreement . In the event of any Pharmacopeia Change in Control during the term of this Agreement, Schering shall have the right to terminate this Agreement upon ninety (90) days written notice after such Pharmacopeia Change in Control. In such event, the provisions of Sections 10.6.1, 10.6.2, 10.6.3 and 10.6.4(d) shall apply, but none of the provisions of Section 10.6.5 shall be applicable.

10.4.2 Termination of the Collaboration . In the event that such Pharmacopeia Change in Control occurs during the term of the Collaboration, Schering may, in its discretion, elect to terminate the Collaboration (but not the Agreement) on ninety (90) days written notice as set forth in Section 2.2.3. Upon receipt of written notice from Schering of its decision to terminate the Collaboration (but not the Agreement) pursuant to this Section 10.4.2 and Section 2.2.3, Pharmacopeia (or its successor in interest as a result of the Pharmacopeia Change in Control) shall have the option (exercisable in its sole discretion) to provide to Schering within thirty (30) days after receipt of such notice a written certification signed by a senior corporate officer of Pharmacopeia (or such successor) setting forth written representations and warranties by Pharmacopeia (or such successor):

 

  (i) that it is committed to continuing in good faith to perform the Collaboration under the terms of this Agreement;

 

  (ii) that it will continue to provide at least the same level and quality of personnel, facilities and resources for the performance of the Collaboration as existed prior to the Pharmacopeia Change in Control;

 

  (iii) that it will implement such additional safeguards as may be required (and which are reasonably acceptable to Schering) to ensure that all of Schering’s Confidential Information will be protected from unauthorized disclosure or use by Pharmacopeia (or such successor) and its Affiliates; and

 

  (iv) that it will take such other actions as are reasonably necessary to provide reasonable assurances to Schering that the results of the Collaboration, including without limitation, any Agreement Compounds and Collaboration Technology, will only be used by Pharmacopeia (or such successor) and its Affiliates in furtherance of the Collaboration or as otherwise expressly permitted under the terms and conditions of this Agreement.

If Pharmacopeia (or such successor) does not provide a certification under this Section 10.4.2 within such thirty (30) day period, then the Collaboration shall terminate upon expiration of the ninety (90) period following Schering’s notice of termination under this Section 10.4.2, and all of the provisions of Section 10.6.5 shall apply.

If Pharmacopeia (or such successor) does provide a certification under this Section 10.4.2 within such thirty (30) day period, then following Schering’s receipt of such certification from Pharmacopeia (or such successor) pursuant to this Section 10.4.2, Schering shall have the right to rescind its notice of termination of the Collaboration by providing written notice to Pharmacopeia within thirty (30) days after receipt of such written certification. If following receipt of such certification, Schering provides written notice rescinding its decision to terminate the Collaboration within such thirty (30) day period, then none of the provisions of Section 10.6

 

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shall apply and the Collaboration shall continue under the terms and conditions of this Agreement as if Schering had never provided any notice of termination under Section 10.4.2. However, if following receipt of such certification, Schering does not provide written notice rescinding its decision to terminate the Collaboration within such thirty (30) day period, then the Collaboration shall terminate upon expiration of the ninety (90) day period following Schering’s notice of termination under Section 10.4.2, and the provisions of Section 10.6.5(i) and (ii) shall apply, but the provisions of Section 10.6.5(iii) shall not apply. For purposes of clarity and avoidance of doubt, the Parties agree that written notice provided by Schering–Plough Ltd. rescinding a decision by Schering-Plough Ltd. to terminate the Collaboration under the corresponding provisions of the International Agreement shall also be deemed notice by Schering under this Agreement.

10.5 Concurrent Termination with the International Agreement . In the event of any termination of the International Agreement by either Pharmacopeia or Schering-Plough Ltd. under the provisions of Sections 10.2, 10.3 or 10.4 thereof, as applicable, this Agreement shall automatically terminate concurrently under the corresponding Section 10.2, 10.3 or 10.4 of this Agreement.

10.6 Effect of Termination .

10.6.1 Accrued Obligations . Termination of this Agreement for any reason shall not relieve the Parties from any liability which at the time of such termination has already accrued to the other Party, or which is attributable to a period prior to such termination, nor preclude either Party from pursuing all rights and remedies it may have hereunder or at law or in equity with respect to any breach of this Agreement.

10.6.2 Return of Materials . Upon any termination of this Agreement, Schering and Pharmacopeia shall promptly return to the other Party all Confidential Information (including without limitation all Existing Schering Know-How or Existing Pharmacopeia Know-How, as the case may be) as set forth in Section 7.3.

10.6.3 Effect on Agreement Products . In the event that two (2) or more Agreement Compounds and/or Agreement Products are being developed and/or commercially exploited by Schering, its Affiliates or Sublicensees under this Agreement and a breach entitling Pharmacopeia to terminate this Agreement occurs which relates solely to a single Agreement Compound or Agreement Product, then Pharmacopeia shall have the option to terminate this Agreement only with respect to the applicable Agreement Compound or Agreement Product, and in which case all of the terms of this Agreement shall remain in full force and effect with regard to the other Agreement Compounds and/or Agreement Products being developed and commercialized. In the event this Agreement is terminated with respect to a given Agreement Product, Schering shall have the right to continue to sell its remaining inventory of such Agreement Product for a period of up to six (6) months after the date of termination, provided that Schering continues to pay royalties to Pharmacopeia with respect to such sales.

10.6.4 Licenses .

(a) Termination by Pharmacopeia Pursuant to Section 10.2 . In the event of termination by Pharmacopeia under Section 10.2, the licenses granted hereunder relating to any Agreement Product with respect to which there has been a material breach, shall terminate, and the licenses granted to Pharmacopeia hereunder shall remain in effect, subject to the terms and conditions of this Agreement; provided , however , a breach shall have no effect on Schering’s licenses hereunder other than with respect to the Agreement Product (together with any Hits, Lead Compounds which are Hits, and/or Derivative Compounds discovered by Pharmacopeia in performance of Screening Programs and/or Optimization Programs against the same Target as such Agreement Product) to which the breach specifically relates, and the remaining licenses granted hereunder shall remain in effect, subject to the terms and conditions of this Agreement.

(b) Termination by Schering Pursuant to Sections 10.2 or 10.3 . In the event of any termination by Schering pursuant to Section 10.2 or 10.3 above, any licenses granted by Schering hereunder shall terminate concurrently, and any licenses granted by Pharmacopeia shall remain in effect, subject to the terms and conditions of this Agreement.

(c) Termination by Pharmacopeia Pursuant to Section 10.3 . In the event of any termination by Pharmacopeia pursuant to Section 10.3 above, any licenses granted by Pharmacopeia hereunder shall terminate concurrently, and any licenses granted by Schering shall remain in effect, subject to the terms and conditions of this Agreement.

 

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(d) Termination by Schering Pursuant to Section 10.4 . In the event of any termination by Schering pursuant to Section 10.4 above, any licenses granted by Pharmacopeia to Schering, and by Schering to Pharmacopeia, shall remain in effect, except for the licenses under Section 4.5, which shall terminate concurrently.

10.6.5 Effect of Termination of the Collaboration for Pharmacopeia Change in Control . In the event that the Collaboration (but not the Agreement) is terminated by Schering pursuant to Sections 10.4.2 and 2.2.3 as a result of a Pharmacopeia Change in Control, and the decision to terminate is not rescinded by Schering in accordance with Section 10.4.2, the Parties further agree that, effective as of *

(i) the non-solicitation provisions of Section 11.8 shall not apply with respect to any of the individual Pharmacopeia employees identified as working on the Collaboration under Section 2.5.1;

(ii) to the extent that Schering contracts with one or more Third Parties to complete any Optimization Program which was ongoing at the time the Collaboration was terminated, Schering shall have the right to *

(iii) if (and only if) Pharmacopeia (or its successor in interest as a result of such Pharmacopeia Change in Control) has failed to timely provide a certification to Schering in accordance with Section 10.4.2, Pharmacopeia (or such successor) *

10.6.6 Surviving Provisions . Articles VI, VII, VIII, IX and XI of this Agreement, as well as Sections 2.9.2, 2.9.3, 2.10, 2.11, 4.1.3, 4.4, 4.7, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 5.10, and 10.6 shall survive the expiration or termination of this Agreement for any reason and shall remain in full force and effect.

ARTICLE XI

MISCELLANEOUS

11.1 Assignment . This Agreement shall not be assigned, or assignable, by either Party hereto to any Third Party without the prior written consent of the other Party, and any such attempted assignment shall be void and without force or effect; provided , however , that notwithstanding the foregoing, either Party may, without such consent, assign this Agreement and its rights and obligations hereunder to an Affiliate or in connection with the transfer or sale of all or substantially all of its business or assets related to the subject matter to which this Agreement pertains, or in the event of its merger, reorganization, acquisition, sale, consolidation or change in control or similar transaction. This Agreement shall be binding upon, and inure to the benefit of, each Party, its Affiliates, and its permitted successors and assigns. Each Party shall be responsible for the compliance by its Affiliates with the terms and conditions of this Agreement.

11.2 Governing Law . This Agreement and any dispute arising from the performance or breach hereof, shall be governed, interpreted and construed in accordance with the laws of the State of New Jersey, without giving effect to conflict of law principles. The Parties expressly exclude application of the United Nations Convention for the International Sale of Goods.

11.3 Dispute Resolution . Except as set forth in Sections 3.3 and 5.5.4, any dispute under this Agreement which is not settled by mutual consent shall be finally settled by binding arbitration, conducted in accordance with the Commercial Arbitration Rules of the American Arbitration Association by three arbitrators appointed in accordance with said rules. The arbitration shall be held in New York, New York and at least one of the arbitrators shall be an independent expert in pharmaceutical product development (including clinical development and regulatory affairs). Any written evidence originally in a language other than English shall be submitted in English translation accompanied by the original or a true copy thereof. The costs of the arbitration, including administrative and arbitrators’ fees, shall be shared equally by the Parties. Each Party shall bear its own costs and attorneys’ and witness’ fees. A disputed performance or suspended performances pending the resolution of the arbitration must be completed within thirty (30) days following the final decision of the arbitrators or such other reasonable period as the arbitrators determine in a written opinion. Any arbitration subject to this Section 11.3 shall be completed within one (1) year from the filing of notice of a request for such arbitration.

 

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11.4 No Implied Licenses . Only the licenses granted pursuant to the express terms of this Agreement shall be of any legal force or effect. No license rights shall be created by implication, estoppel or otherwise.

11.5 Representation by Legal Counsel . Each Party hereto represents that it has been represented by legal counsel in connection with this Agreement and acknowledges that it has participated in the drafting hereof. In interpreting and applying the terms and provisions of this Agreement, the Parties agree that no presumption shall exist or be implied against the Party which drafted such terms and provisions.

11.6 Waiver . Any delay or failure in enforcing a Party ’s rights under this Agreement or any waiver as to a particular default or other matter shall not constitute a waiver of such Party s rights to the future enforcement of its rights under this Agreement, nor operate to bar the exercise or enforcement thereof at any time or times thereafter, excepting only as to an express written and signed waiver as to a particular matter for a stated duration.

11.7 Independent Contractors . The relationship of the Parties hereto is that of independent contractors. Nothing herein contained shall be deemed to create an employment, agency, joint venture or partnership relationship between the Parties hereto or any of their agents or employees. Neither Party shall have any power to enter into any contracts or commitments or to incur any liabilities in the name of, or on behalf of, the other Party, or to bind the other Party in any respect whatsoever.

11.8 Solicitation of Employees . Schering and Pharmacopeia both agree that, during the Collaboration Term and for one (1) year thereafter, without the express prior written consent of the other Party, they will not knowingly induce or attempt to induce, directly or indirectly, any scientific or technical personnel then employed by the other Party to accept employment or affiliation with the inducing Party or its Affiliates.

11.9 Compliance with Laws . In exercising their rights under this license, the Parties shall fully comply with the requirements of any and all applicable laws, regulations, rules and orders of any governmental body having jurisdiction over the exercise of rights under this license.

11.10 Export Control . This Agreement and the obligations of both Parties hereunder are made subject to, and limited by, all applicable restrictions concerning the export of products or technical information from the United States of America which may be imposed upon or related to Pharmacopeia or Schering from time to time by the government of the United States of America. Furthermore, Schering agrees that it will not export, directly or indirectly, any technical information acquired from Pharmacopeia under this Agreement or any products using such technical information to any country for which the United States government or any agency thereof at the time of export requires an export license or other governmental approval, without first obtaining the written consent to do so from the Department of Commerce or other agency of the United States government when required by an applicable statute or regulation.

11.11 Patent Marking . Schering agrees to mark and have its Affiliates and Sublicensees mark all Agreement Products sold pursuant to this Agreement in accordance with the applicable statute or regulations relating to patent marking in the country or countries of manufacture and sale thereof.

11.12 Notices . Any notice required or permitted to be given or sent under this Agreement shall be in writing and shall be hand delivered or sent by express delivery service or certified or registered mail, postage prepaid, or by facsimile transmission (with written confirmation copy by registered first-class mail) to the Parties at the addresses and facsimile numbers indicated below.

 

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If to Pharmacopeia, to:

Pharmacopeia, Inc.

3000 Eastpark Boulevard

Cranbury, New Jersey 08512

Attn: Chief Executive Officer

Fax No.: (609) 452-3672

with a copy to:

Pharmacopeia, Inc.

3000 Eastpark Boulevard

Cranbury, New Jersey 08512

Attn: General Counsel

Fax No.: (609) 452-3655

If to Schering, to:

Schering Corporation

2000 Galloping Hill Road

Kenilworth, New Jersey 07033

Attention: Vice President, Business Development

Facsimile No.: (908) 298-5379

with copies to:

Schering Corporation

2000 Galloping Hill Road

Kenilworth, New Jersey 07033

Attention: Law Department, Senior Legal Director – Licensing

Facsimile No.: (908) 298-2739

Schering-Plough Ltd.

Toepferstrasse 5

CH 6004 Lucerne, Switzerland

Attention: President

Facsimile No.: (011) 41 41 418 1630

Any such notice shall be deemed to have been given when received. Either Party may change its address or its facsimile number by giving the other Party written notice, delivered in accordance with this Section.

11.13 Force Majeure . Failure of any Party to perform its obligations under this Agreement (except the obligation to make payments when properly due) shall not subject such Party to any liability or place them in breach of any term or condition of this Agreement to the other Party to the extent (and only to the extent) that such failure is due to fire, explosion, flood, drought, war, terrorism, riot, sabotage, embargo, strikes or other labor trouble, failure of suppliers, a national health emergency, compliance with any order or regulation of any government entity acting with color of right, or any other cause beyond the reasonable control of such non-performing Party and not caused by the negligence, intentional conduct or misconduct of the non-performing Party (such event or cause referred to as “force majeure”). The Party affected shall promptly notify the other Party of the condition constituting force majeure as defined herein and shall exert reasonable efforts to eliminate, cure or overcome any such event of force majeure and to resume performance of its obligations with all possible speed. If a condition constituting force majeure as defined herein exists for more than ninety (90) consecutive days, the Parties shall meet to negotiate a mutually satisfactory resolution to the problem, if practicable. The foregoing notwithstanding, nothing herein shall require any Party to settle on terms unsatisfactory to such Party any strike, lock-out or other labor difficulty, any investigation or proceeding by any public authority or any litigation by any Third Party.

 

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11.14 Severability . If any provision of this Agreement becomes or is declared by a court of competent jurisdiction to be illegal, invalid or unenforceable or void, it is mutually agreed that this Agreement shall remain in full force and effect without such provision, and the Parties will, in good faith, renegotiate the terms and conditions of this Agreement so as to lawfully include the substance of such provision (to the extent possible) in order to as fully as possible realize the intent of the Parties and their commercial bargain.

11.15 Counterparts . This Agreement may be executed in any number of counterparts, each of which shall be an original as against either Party whose signature appears thereon, but all of which taken together shall constitute but one and the same instrument, and shall become effective on the Effective Date.

11.16 Captions . The captions of this Agreement are solely for the convenience of reference and shall not affect its meaning or interpretation.

11.17 Complete Agreement . This Agreement with its Exhibits, together with the International Agreement, constitutes the entire agreement between the Parties with respect to the subject matter hereof, and all prior agreements respecting the subject matter hereof, either written or oral, expressed or implied, shall be abrogated, canceled, and are null and void and of no effect; provided , however that except as expressly set forth in this Agreement, nothing herein shall affect the rights and obligations of the Parties under: (i) the certain Collaboration Agreement and the certain Random Library Agreement between Pharmacopeia, Schering Corporation and Schering-Plough Ltd. effective as of December 22, 1994, as amended (the “1994 Agreements”); or (ii) the certain contemporaneous Collaboration Agreements between Pharmacopeia and each of Schering Corporation and Schering-Plough Ltd., effective as of October 29, 1998, each as amended (the “1998 Agreements”). No amendment, modification, supplement, change or addition to this Agreement (or the Exhibits attached hereto) shall be effective or binding on either of the Parties hereto unless reduced to writing and executed by the respective duly authorized representatives of Pharmacopeia and Schering.

11.18 Relationship of Prior Agreements . For purposes of clarity and avoidance of doubt, the Parties acknowledge and agree that the terms and conditions of this Agreement shall not apply to any compounds or products discovered and developed by or on behalf of the Parties under the 1994 Agreements or the 1998 Agreements. In particular, the Parties acknowledge and agree that (i) no milestone payment or royalty obligations set forth in this Agreement shall apply to any compounds discovered and/or developed under the 1994 Agreements or the 1998 Agreements, and (ii) any Agreement Compounds and/or Agreement Products discovered and developed under this Agreement shall not be subject to any milestone payment or royalty obligations set forth in the 1994 Agreements or the 1998 Agreements.

11.19 Recording . Each Party shall have the right, at any time, to record, register, or otherwise notify this Agreement in appropriate governmental or regulatory offices anywhere in the world, and each Party shall provide reasonable assistance to the other in effecting such recording, registering or notifying. The Parties acknowledge that this Agreement may be notified by either Party to the European Community for compliance with applicable laws.

11.20 Further Actions . Each Party agrees to execute, acknowledge and deliver such further instruments, and to do all other acts, as may be necessary or appropriate in order to carry out the purposes and intent of this Agreement including, without limitation, any filings with any antitrust agency which may be required.

IN WITNESS WHEREOF, this Agreement has been executed by the duly authorized representatives of the Parties as of the date set forth below.

 

PHARMACOPEIA, INC.     SCHERING CORPORATION
By:  

/s/    Stephen A. Spearman

    By:  

/s/    David Poorvin

Title:   EVP     Title:   Vice President
Date:   7/9/03     Date:   7/9/03

 

34


EXHIBIT A

CURRENCY CONVERSION


*


EXHIBIT C

Elements of Fully Allocated Manufacturing Costs

The following expenses are included in manufacturing costs:

 

  1. Direct Materials

Materials used in the manufacturing process that are traced directly to the completed product, such as:

 

   

Inert raw materials or excipients

 

   

Active substances/ingredients

 

   

Packaging components such as bottles, caps, labels, etc.

 

  2. Direct Labor

The cost of employees engaged in production activities that are directly identifiable with product costs. Excludes supervision, which is included in indirect labor, and production support activities such as inspection, plant and equipment maintenance labor, and material handling personnel. Direct Labor cost includes:

 

   

Base pay, overtime, vacation and holidays, illness, personal time with pay, and shift differential.

 

   

Cost of employee fringe benefits such as health and life insurance, payroll taxes, welfare, pension, profit sharing and bonuses.

 

  3. Indirect Manufacturing Costs

Costs which are ultimately allocated to product based on an appropriate method such as standard direct labor hours, tank hours, grams, vials, etc., of the operating departments. These costs include:

 

   

Indirect Production Labor - salaries of employees engaged in production activities who are not classified as direct labor, including supervision, clerical, etc.

 

   

Costs of Direct Labor - employees not utilized for the manufacturing of product such as training, downtime and general duties.

 

   

Indirect Materials - supplies and chemicals which are used in the manufacturing process and are not assigned to specific products but are included in manufacturing overhead costs. Includes supplies for which direct assignment to products is not practical.

 

   

Utilities - expenses incurred for fuel, electricity and water in providing power for production and other plant equipment.

 

   

Maintenance and Repairs - amount of expense incurred in-house or purchased to provide services for plant maintenance and repairs of facilities and equipment.

 

   

Other Services - purchased outside services and rentals such as the cost of security, ground maintenance, etc.


   

Depreciation - of plant and equipment utilizing the straight-line method of calculation.

 

   

Insurance - cost of inventory insurance, comprehensive insurance and other insurance necessary for the safeguard of manufacturing plant and equipment.

 

   

Taxes - expense incurred for taxes on real and personal property (manufacturing site, buildings and the fixed assets of equipment, furniture and fixtures, etc.). If manufacturing site includes other operations (marketing, R&D, etc.), taxes are allocated to manufacturing on the basis of total real and personal property.

 

   

Cost of manufacturing, service departments - such as: (where applicable)

 

   

Packaging Engineering

 

   

Manufacturing Maintenance

 

   

Industrial Engineering

 

   

Receiving and Warehousing

 

   

Purchasing and Accounting

 

   

Production Scheduling

 

   

Inventory Management

 

   

Plant Materials Management

 

   

Central Weigh

 

   

Manufacturing Administration

 

   

Regulatory Affairs direct support to manufacturing (not to exceed $80,000 per year for a three(3) year period)

 

   

Allocated costs of services provided to manufacturing including: (where applicable)

 

   

Cafeteria

 

   

Personnel Operations

 

   

Health and Safety Services

 

   

Division Engineering and Operations Services

 

   

Plant Services (housekeeping)

 

   

Manufacturing Information Systems


   

Plant Power

 

   

Office of V.P. Manufacturing

Various bases are used for allocating these costs to manufacturing operating departments including headcount, square feet, metered utilities use, estimated services rendered, EDP computer hours, etc.

 

4. Quality Assurance Costs

Direct labor and indirect costs for Quality Assurance departments testing and approving materials used in manufacturing and completed manufacturing batches and finished products. This includes all manufacturing in-process testing and testing of finished materials. Excluded from product costs are QA costs related to research and development, stability testing, etc.

The following expenses are not included in manufacturing costs:

 

  a) Inventory Carrying Costs

 

  b) Regulatory Affairs Costs (except as set forth above)

 

  c) Pilot plant costs, research batches and other similar costs prior to turnover to manufacturing. These are handled as development costs and expensed to R&D. This excludes commercial goods produced by a research facility.

 

  d) Costs incurred by Manufacturing for special projects, or for Schering-Plough Research Institute requests, to establish and certify new production processes, batch sizes and product line improvements, and new vendor certification of equipment and primary materials components. These costs are expensed to R&D.

 

  e) Manufacturing start-up costs and initial one-time extraordinary manufacturing costs incurred prior to plant operation and achievement of a normal production activity level. Includes costs of training, testing, qualification/validation of new equipment and facilities and initial trial batches. These costs are deferred and then amortized to Other Production Costs over five years.

 

  f) Significant idle capacity is eliminated from factory overhead and product cost. Idle or excess capacity costs are culled out of the Manufacturing Budget and expensed as a period cost to Other Production Costs.

 

  g) Finished goods warehousing, shipping and other distribution costs. These are included in distribution costs which are part of marketing expenses.

 

  h) Product liability and/or business interruption insurance expenses.

Exhibit 10.327

LEASE AGREEMENT

BY AND BETWEEN:

Eastpark at 8A

“Landlord”

- and -

Pharmacopeia, Inc.

“Tenant”

PREMISES: 1002 Eastpark Boulevard Cranbury, NJ 08512

DATED: August 20, 2003


TABLE   OF   CONTENTS

 

1.    LEASED PREMISES
2.    TERM OF LEASE
3.    CONSTRUCTION OF THE TENANT IMPROVEMENTS
4.    RENT
5.    PARKING AND USE OF EXTERIOR AREA
6.    USE
7.    REPAIRS AND MAINTENANCE
8.    COMMON AREA EXPENSES, TAXES AND INSURANCE
9.    SIGNS
10.    ASSIGNMENT AND SUBLETTING
11.    FIRE AND CASUALTY
12.    COMPLIANCE WITH LAWS, RULES AND REGULATIONS
13.    INSPECTION BY LANDLORD
14.    DEFAULT BY TENANT
15.    LIABILITY OF TENANT FOR DEFICIENCY
16.    NOTICES
17.    NON-WAIVER BY EITHER PARTY
18.    RIGHT OF TENANT TO MAKE ALTERATIONS AND IMPROVEMENTS
19.    NON-LIABILITY OF LANDLORD
20.    RESERVATION OF EASEMENT
21.    STATEMENT OF ACCEPTANCE
22.    FORCE MAJEURE
23.    STATEMENTS BY LANDLORD AND TENANT
24.    CONDEMNATION
25.    LANDLORDS REMEDIES
26.    QUIET ENJOYMENT
27.    SURRENDER OF PREMISES
28.    INDEMNITY
29.    BIND AND CONSTRUE CLAUSE
30.    INCLUSIONS
31.    DEFINITION OF TERM “LANDLORD”
32.    COVENANTS OF FURTHER ASSURANCES
33.    COVENANT AGAINST LIENS
34.    SUBORDINATION
35.    EXCULPATION OF LANDLORD
36.    NET RENT
37.    SECURITY
38.    BROKERAGE
39.    LATE CHARGES
40.    PRESS RELEASES
41.    WAIVER OF JURY TRIAL
42.    LAWS OF NEW JERSEY
43.    OPTION TO RENEW
44.    RIGHT OF FIRST REFUSAL
45.    CROSS DEFAULT

 

i


AGREEMENT, made August 20,2003, between Eastpark at 8A, 1000 Eastpark Blvd., Cranbury, New Jersey 08512, “Landlord”; and Pharmacopeia, Inc., 3000 Eastpark Boulevard, Cranbury, NJ 08512, “Tenant”.

WITNESSETH

WHEREAS, the Landlord intends to lease to the Tenant Suite #1002 with an address at 1002 Eastpark Boulevard, Cranbury, NJ 08512, in Building 1000 (“Building”) which constitutes a portion of the office/industrial park known as Eastpark at 8A (“Office Park); and

WHEREAS, the parties hereto wish to mutually define their rights, duties and obligations in connection with the Lease;

NOW THEREFORE, in consideration of the promises set forth herein, the Landlord leases unto the Tenant and the Tenant rents from the Landlord the leased premises described in Paragraph 1, and the Landlord and Tenant do hereby mutually covenant and agree as follows:

 

1. LEASED PREMISES

The leased premises shown on Exhibit “A” shall consist of 18,191 rentable square feet of office and laboratory space (“Leased Premises”) as measured from outside of exterior walls to center line of the common walls, together with all improvements to be constructed thereon by the Landlord for the use of the Tenant, and all easements, tenements, appurtenances, hereditaments, rights and privileges appurtenant thereto, and any and all fixtures and equipment which are to be installed in the Building by the Landlord for the use of the Tenant in its occupancy of the Leased Premises. Tenant shall also have the right to use all common areas of the Office Park in a similar manner as other Office Park tenants.

 

2. TERM OF LEASE

The term of the Lease shall be 12 years and shall be co-terminus with a lease for Building #3, which is also to be occupied by Tenant. The rent shall commence upon Substantial Completion (as defined hereafter). The 12 year term shall commence on the first day of the month following the date on which Substantial Completion is achieved for both Buildings 1 and 3, and shall expire on the day before the 12th anniversary of the Commencement Date, it being the intent of the parties that the leases for both Buildings shall expire on the same date. The Commencement Date is projected to be January 15, 2004.

 

3. CONSTRUCTION OF THE TENANT IMPROVEMENTS

3.1 The Leased Premises consists of two existing, contiguous spaces which were previously leased to other tenants. Tenant is taking the Leased Premises in its “as is” condition, subject to modifications as shown on the Plans (as hereafter defined) to be prepared by Tenant (“Tenant Improvements”). The Landlord shall provide all necessary labor and materials and perform all the work required to complete the Tenant Improvements in order to ready the same for Tenant’s occupancy. Tenant’s designated representative for all work pertaining to the Tenant Improvements shall be John Harrison or such other person as is designated in writing by Tenant (“Representative”). The Landlord shall supervise and direct the work on the Tenant Improvements using Landlord’s best skill and attention, and Landlord shall be solely responsible for all construction means, methods, techniques, sequences and procedures and for coordinating all portions of the work on the Tenant Improvements. Landlord warrants to the Tenant that all materials and equipment incorporated in the Tenant Improvements will be new unless otherwise specified, and that all work on the Tenant Improvements will be of good quality, free from known faults and defects, and in substantial conformity with the Plans.

 

  3.2

(a) Landlord shall complete the Tenant Improvements in a good and workmanlike manner and in substantial accordance with plans and specifications (“Plans”) to be prepared by Tenant’s architect, CUH2A. The Plans shall be provided to Landlord on or before September 1, 2003 and shall be in sufficient detail to permit Landlord to apply for a building permit for the Tenant Improvements (which Landlord shall promptly do), and to prepare a construction budget for the

 

1


 

construction of the Tenant Improvements (“Construction Budget”). In the event Tenant does not deliver the Plans to Landlord by the date set forth above, such failure shall not delay the date for commencement of the rent, which shall be presumed to be the projected Commencement Date set forth in paragraph 2. The Construction Budget shall set forth the lump sum amount payable by Tenant to Landlord for the construction of the Tenant Improvements, which amount shall include Landlord’s standard mark-up for general conditions, overhead and profit, which total in the aggregate 20%. The only exception to the lump sum amount shall be the actual fees charged by the Township of South Brunswick for construction permits in connection with the Tenant Improvements, which sums shall be paid by Tenant as set forth hereafter. Landlord shall submit the Construction Budget to Tenant for its approval. Tenant shall give written notice to Landlord within five business days of receipt, as to whether or not the Construction Budget is acceptable. If Tenant does not accept the Construction Budget during such five business day period, then the parties agree to negotiate in good faith to reach an agreement on the Construction Budget. Landlord shall not be obligated to order any equipment or commence work until Tenant has approved the Construction Budget. A complete set of the agreed upon Plans, and the agreed upon Construction Budget, shall be initialed by and distributed to Landlord and Tenant.

(b) Neither the Construction Budget nor the Plans shall be changed or altered in any way except by change order approved in writing by Landlord and Tenant (“Change Order”). All Change Orders shall be valid and binding upon Landlord and Tenant only if authorized by written Change Order signed by Landlord and Tenant’s Representative prior to commencement of the work on the Tenant Improvements reflected thereby. The cost or credit to the Tenant due to any Change Order shall be determined per the terms of such Change Order. In the event the Change Order increases the cost set forth in the Construction Budget, then Landlord shall submit an invoice to Tenant and Tenant shall pay the invoice upon completion of work or upon the ordering of any equipment, whichever is applicable. The Landlord shall have the right to substitute for the materials and equipment required by the Plans, materials and equipment of equal quality and standard, provided said substitutions conform with applicable building codes and are the subject of a Change Order. Each and every Change Order shall state whether the change will entail a delay in the date of Substantial Completion. Any Change Order requested by Tenant which results in a delay to the date of Substantial Completion shall not delay the date for the commencement of the payment of rent.

 

  3.3 (a) The Landlord may secure and advance payment for the construction permits and for all other permits and governmental fees, licenses and inspections necessary for the proper execution and completion of the Tenant Improvements. Tenant shall pay such amounts to Landlord not later than 10 business days after receipt of an invoice therefore Landlord shall not, however, be responsible for securing any environmental or operating permits or certifications which are required in order for Tenant to actually conduct its business.

(b) Tenant shall be responsible for providing Landlord with, and bearing the cost of sufficient copies of the Plans, and sufficient copies of any revisions made to the Plans, in order to obtain the permits and efficiently manage the construction of the Tenant Improvements. In the event any Change Orders are required during construction, Tenant shall be responsible for all costs related to the preparation and reproduction of plans therefore, unless the Change Order was solely initiated by Landlord, in which case Landlord shall be responsible for such costs. After construction is complete, Tenant shall be responsible for all costs related to the reproduction of “as built” Plans. In all instances where Plans are required, Tenant shall provide Landlord with a reproducible set. Landlord will also be provided with a current plot file containing the Plans at no cost to Landlord. Tenant agrees to have its Architect execute Exhibit “A” affirming Landlord’s right to the Plans.

 

  3.4

(a) Tenant shall pay Landlord directly for the construction costs of Tenant Improvements in accordance with the schedule attached hereto as Exhibit “B”. The only exception to Tenant’s responsibility to pay for all construction costs shall be for the work necessary to upgrade the existing HVAC reheat system currently in the space previously occupied by Biomira, Inc.

 

2


 

(currently known as 1002 Eastpark Boulevard), which cost is estimated to be $150,000 and will he divided equally between the parties. In the event Tenant fails to pay to Landlord any sum set forth on Exhibit “B” when it is due, Landlord shall not be obligated to commence or continue work on the Tenant Improvements. Such failure to pay shall constitute a default under this Lease, but shall not delay the Commencement Date of this Lease, which shall be presumed to be the projected Commencement Date set forth in paragraph 2; or any of Tenant’s obligations hereunder including, without limitation, Tenant’s obligation to pay all Rent. In the event that Tenant fails to pay to Landlord, upon Substantial Completion of the Tenant Improvements, a sum equal to the remaining balance then due, such failure shall constitute a default under this Lease; and Tenant shall not be permitted to occupy the Leased Premises; and Tenant shall commence payment of all Rent; and Landlord shall be entitled to all rights and remedies available hereunder, at law or in equity, which rights shall be cumulative. All sums so owing to Landlord shall constitute Additional Rent and shall be subject to the imposition of late charges as provided in this Lease.

(b) Apart from extensions of time for delays and extensions of the date for the payment of rent, no payment or allowance of any kind shall be claimed by Tenant, or made to the Landlord as compensation for damages on account of any delay from any cause in the completion of the Tenant Improvements, whether such delay be avoidable or unavoidable, anything in this Agreement inconsistent herewith or to the contrary notwithstanding.

3.5 Tenant shall be responsible for the design and installation of its own phone, data and communication systems which systems shall be installed in a manner not to interfere with Landlord’s construction efforts. During construction of Tenant Improvements, a representative of Tenant shall inspect the site no less frequently than once a week and verify and agree that the work in progress has been completed in a manner acceptable to Tenant.

3.6 The Tenant Improvements shall be commenced upon issuance of the building permit by governmental entities having jurisdiction therefor and, subject to authorized adjustments, Substantial Completion is estimated to be achieved on or about January 15 2004. As used herein the term “Substantial Completion” shall mean that the Leased Premises have been built and completed in substantial conformity with the Plans, and a temporary or permanent certificate of occupancy or a temporary or permanent certificate of acceptance (“CO/CA”) has been issued permitting Tenant to use and occupy the Leased Premises, even though minor details, adjustments or punch list items which shall not materially impair Tenant’s use and enjoyment of the Leased Premises may not have been finally completed, but which work Landlord agrees shall be diligently pursued to final completion. Tenant shall allow Landlord and its contractors to enter the Leased Premises during normal working hours after issuance of the CO/CA to complete remaining minor work or punch list items, provided Landlord gives advance notice and makes reasonable efforts not to interfere with Tenant’s operations. It is agreed that for the purpose of this Lease, wherever and whenever the term Substantial Completion is used, it shall not include items of maintenance, service, punch list, or guarantee. If the date of Substantial Completion occurs on a day other than the first day of a month, rent from such day until the first day of the following month shall be prorated (at a rate of 1/30th of the monthly rent per day). During said period of partial monthly occupancy, all other terms and conditions of this Lease shall apply.

 

4. RENT

 

  4.1 Tenant shall pay, as base rent (“Base Rent”) for the Leased Premises, as follows:

(a) During the first 4 years of the term, an estimated annual base rent per square foot of $30.35, for an aggregate annual base rent of $552,096.85 (“Initial Base Rent”), payable monthly in the sum of $46,008.07.

 

3


(b) During the second 4 years of the term, the Base Rent shall be increased by adding to the Initial Base Rent the increase in the Consumer Price Index (“CPI”) as follows, and such sum shall be the Base Rent for the second 4 years of the term (the “Adjusted Base Rent”):

The “All Items” Index Figures for the New York-Northeastern New Jersey average of the “Consumer Price Index for All Urban Consumers” (revised CPI-U) (1982-1984 equal to 100) published by the Bureau of Labor Statistics of the U.S. Department of Labor (“Index”) for the month 2 months prior to the date of Substantial Completion shall be compared with the same index for the month 2 months prior to the beginning month of the second 4 years of the Lease term. If there is an increase in the Index that percentage increase shall be used to determine the rent increase over the original Base Rent, as shown in the following example:

If the Index figure for the month 2 months prior to the date of Substantial Completion is 100 (the denominator) and the Index figure for the month 2 months prior to the beginning of the second 4 years of the lease term is 110, the increase in the Index figures will produce an increase of 10%.

 

  (110-100)   = 10%  
  100    

Applying the formula, 10% of $552,096.85 is equal to $55,209.69. Adding that amount to the original Base Rent produces an annual rent for the second 4 years of $607,306.54 payable in equal monthly installments of $50,608.88.

However, in no event shall the increase in rent be more than 12%.

(1) In the event that the Index figure is discontinued the parties shall agree on an equivalent and substituted Cost of Living Index to be applied in the same manner. In the event the parties cannot mutually agree as to a substituted Index, then the issue shall be submitted for arbitration to the American Arbitration Association to take place in South Brunswick or any of its contiguous municipalities, with the cost thereof divided between the parties.

(2) If the base year (1982-84 equal to 100) herein above referred to with respect to the “Index” shall be changed after the execution of the Lease, appropriate adjustments based on such new Index shall be made so as to have a proper application of the Cost of Living formula.

(c) During the third 4 years of the term, the Base Rent shall increase according to the same CPI formula set forth above using the Adjusted Base Rent, but not more than 12 % over the Adjusted Base Rent for the second 4 years.

4.2 In addition to the Base Rent, Tenant shall pay as additional rent (“Additional Rent”) all real estate taxes for the Property, plus its proportionate share of the repairs, maintenance, insurance and any other charges allocated amongst tenants, as more specifically described in paragraph 8 (“Common Area Expenses”), based on the relationship between the rentable square footage leased to Tenant and the rentable square footage of building construction completed and occupied in the Office Park. Tenant’s Common Area Expenses shall be adjusted as of each January 1st during the term based on the increase in Common Area Expenses set forth in paragraph 8.

4.3 The Base Rent and Additional Rent shall be referred to hereafter as “Rent”.

4.4 Tenant covenants to pay the Rent in lawful money of the United States which shall be legal tender for the payment of all debts, public and private, at the time of payment. Such Rent shall be paid to Landlord at its office address hereinabove set forth, or at such other place as Landlord may, from time to time, designate by notice to Tenant.

4.5 Rental payments shall be payable in advance in equal monthly installments on the first day of each calendar month. The Rent shall be payable by Tenant without any set-off or deduction of any kind or nature whatsoever and without notice or demand. The sum of all increases required to be paid as Additional Rent or Base Rent in accordance with this Lease, shall be paid to Landlord within 10 days following the giving of notice hereof by Landlord of such increases.

 

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5. PARKING AND USE OF EXTERIOR AREA

The Tenant shall have the right to use parking spaces on a non-exclusive basis in common with other tenants of the Building. Landlord reserves the right to allocate specific parking spaces if it chooses. The Landlord and Tenant mutually agree that they will not block, hinder or otherwise obstruct the access driveways and parking areas so as to impede the free flow of vehicular traffic in the Office Park. In connection with the use of the loading platforms, if any, Tenant agrees that it will not use the same so as to unreasonably interfere with the use of the access driveways and parking areas. Tenant shall not store trailers or other vehicles on any portion of the access driveways or parking areas, and may not utilize any portion of the land or Building outside of the Leased Premises for any purpose unless consented to in advance by Landlord.

 

6. USE

The Tenant covenants and agrees to use and occupy the Leased Premises only as an office and laboratory, which use is expressly subject to all applicable zoning ordinances, rules and regulations of any governmental instrumentalities, boards or bureaus having jurisdiction thereof. Tenant’s use of the Leased Premises shall not interfere with the peaceable and quiet use and enjoyment by other tenants at their respective leased premises located at the Building or in the Office Park, nor shall Tenant’s activities cause Landlord to be in default under its leases with such other tenants.

 

7. REPAIRS AND MAINTENANCE

7.1 Tenant shall generally maintain and repair the Leased Premises, in a good and workmanlike manner, and shall, at the expiration of the term, deliver the Leased Premises in good order and condition, damages by fire or casualty, the elements and ordinary wear and tear excepted. Tenant covenants and agrees that it shall not cause or permit any waste, damage or disfigurement to the Leased Premises, or any overloading of the floors. Tenant shall maintain and make all repairs to the floor surface, plumbing and electrical systems including all ballasts and fluorescent fixtures located within the Leased Premises, and the entire HVAC system. Landlord shall be responsible for repairs necessary to the roof, exterior and load-bearing walls, and electric and plumbing systems to the point where they enter the Leased Premises, unless repair is necessitated by any act of Tenant, or its agents, employees or contractors.

7.2 The Tenant shall, at its own cost and expense, pay all utility meter and service charges, including gas, water and electric servicing the Leased Premises. Landlord shall have the option to install, at its own cost, a separate water meter and invoice Tenant directly for its water usage. The Tenant agrees to maintain all leased areas at a minimum temperature of 45 degrees, excluding cold rooms on other rooms specifically designed for a lower temperature, to prevent the freezing of domestic water and sprinkler pipes. Tenant shall not store any items outside the Leased Premises, and shall deliver its garbage and recyclables to the central receiving area on the lot. Tenant shall dispose of all hazardous/medical waste with an approved hauler at its own cost.

7.3 Landlord does not warrant that any services Landlord or any public utilities supply will not be interrupted. Services maybe interrupted because of accidents, repairs, alterations, improvements or any other reason beyond the reasonable control of Landlord, not including the gross negligence of Landlord or its agents.

 

8. COMMON AREA EXPENSES. TAXES AND INSURANCE

8.1 The Tenant shall pay to the Landlord, monthly, as Additional Rent its Proportionate Share of the following items all of which shall be known as Common Area Expenses:

(a) The costs incurred by the Landlord for the operation, maintenance or repair of the following items in the Office Park, (“Operating Costs”):

(1) lawns and landscaping;

 

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(2) standard water usage and standby sprinkler charges;

(3) exterior lighting;

(4) exterior sewer lines;

(5) exterior utility lines;

(6) repair and maintenance of any signs serving the Office Park;

(7) snow removal;

(8) standard garbage disposal and recycling;

(9) general ground maintenance;

(10) parking lot, driveways and walkways;

(11) maintenance contracts for the roof;

(12) pest control;

(13) central station monitoring for fire sprinkler system; and

(14) other ordinary maintenance expenses normally incurred by Landlord relating to the Building and common areas of the Office Park.

Notwithstanding the above, the following items shall be excluded from Common Area Expenses:

(a) Cost of decorating, redecorating, cleaning or other services not provided on a regular basis to the tenants of the Office Park;

(b) Wages, salaries, fees and fringe benefits paid to administrative or executive personnel or officers or partners of Landlord, unless employed at competitive rates as independent contractors at the building or Office Park

(c) All cost relating to activities for the solicitation, negotiation and execution of leases of space in the Office Park;

(d) Cost of any repair made by Landlord because of the total or partial destruction of the building or the condemnation of a portion of the building;

(e) Any insurance premium for which Landlord is to be reimbursed by Tenant, pursuant to this Lease, or by any other tenant of the Office Park;

(f) Depreciation, interest or rents paid or incurred by Landlord;

(g) Any charge to Landlord for income taxes, franchise taxes or similar taxes;

(h) Collection costs for bad debt expenses not related to Tenant;

 

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(i) Cost of tenant improvements;

(j) Legal, accounting, bank or other fees incurred in connection with any equity or debt financing or sale of the building or Office Park;

(k) Costs of specialized services provided to other tenants but not provided to tenants generally;

(l) Capital expenditures;

(m) Cost to comply with ADA related to the interior of the individual buildings, but not exterior doors or the Office Park;

(n) Costs to cure violations of law or ordinances;

(o) Electric for non-public areas.

(b) The cost of the annual insurance premiums charged to the Landlord for insurance coverage which insure the buildings in the Office Park. The insurance shall be for the full replacement value of all insurable improvements with any customary extensions of coverage including, but not limited to, vandalism, malicious mischief, sprinkler damage and comprehensive liability, and insurance for one years rent. The Landlord shall maintain said insurance in effect at all times hereunder. Any increase in the insurance premiums due to a change in rating of the Building which is solely attributable to Tenants use, or due to special Tenant equipment, shall be paid entirely by the Tenant. Tenant expressly acknowledges that Landlord shall not maintain insurance on Tenants furniture, fixtures, machinery, inventory, equipment or other personal property; and

(c) The real estate and personal property taxes assessed against the Office Park for land, building and improvements, along with any levy for the installation of local improvements affecting the Office Park assessed by any governmental body having jurisdiction thereof. Tenant shall he entitled to Tenant’s Proportionate Share of any refund obtained by Landlord with respect to any taxes. The real estate tax obligation of the Tenant shall include any tax or imposition for parking lot usage which may be levied by any governmental body having jurisdiction thereof. In addition to its Proportionate Share of the above items, Tenant shall pay directly all real estate taxes assessed by the municipality on its Tenant Improvements. Anything in this Section 8.1(b) or elsewhere in this Lease to the contrary notwithstanding, Tenant shall not be obligated to pay any part of (l) any taxes on the income of the Landlord or the holder of an underlying mortgage and any taxes on the income of the lessor under any underlying lease, (2) any corporation, unincorporated business or franchise taxes, (3) any estate, gift, succession or inheritance taxes, (4) any capital gains, mortgage recording or transfer taxes, (5) any taxes or assessments attributable to any sign attached to, or located on, the Building or the land or (6) any similar taxes imposed on the Landlord, the holder of any underlying mortgage or the lessor under any underlying lease; and

(d) A management fee of 3% of the Tenants Base Rent.

8.2 Within 90 days of the expiration of the first calendar year of the Term, the Landlord shall furnish to Tenant a detailed breakdown of the actual Common Area Expenses. Tenant shall have the right, within 30 days of receipt of the breakdown, and during normal business hours, to examine Landlord’s books and records with respect to the Common Area Expenses. In the event Tenant’s Proportionate Share shall be greater than the aggregate paid by the Tenant during the prior period, Tenant shall pay any difference, in one lump sum within 30 days after demand. In the event Tenant shall have overpaid its Proportionate Share, any such overage shall be applied to the Base Rent and Additional Rent prospectively due under the Lease. This procedure shall be followed during each year of the lease term, and at the expiration of the Lease, any overage or underage shall be credited or paid after computation by the Landlord, which obligation of Landlord and Tenant shall survive the expiration of the lease term.

 

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8.3 Tenant’s Share of Common Area Expenses for any calendar year, part of which falls within the term of this Lease and part of which does not, shall be appropriately prorated.

8.4 If at any time during the term of this Lease the method or scope of taxation prevailing at the commencement of the lease term shall be altered, Tenant’s Proportionate Share of such substituted tax or imposition shall be payable and discharged by the Tenant in the manner required pursuant to the law which shall authorize such change.

8.5 The Tenant covenants and agrees that it will, at its sole cost and expense, carry liability insurance covering the Leased Premises in the minimum amount of $1,000,000.00 per accident for 1 person, $3,000,000.00 per accident for 2 or more persons, and a minimum amount of $300,000.00 for property damage. Tenant shall at all times, carry sufficient insurance to avoid any coinsurance penalties on Tenant’s furniture, furnishings, fixtures, machinery, equipment and installations as well as on any alterations or improvements made to the Leased Premises by Tenant subsequent to the Commencement Date. Such coverage is to include all additions and alterations contemplated hereunder, and shall cover the value of equipment and supplies awaiting installation. The Tenant shall add the Landlord as an additional insured on such policy and will furnish Landlord with a certificate of said liability insurance prior to the Commencement Date and annually thereafter. The certificate shall contain a clause that the policy will not be canceled except on 10 days written notice to the Landlord.

8.6 The parties covenant and agree that the insurance policies required to be furnished in accordance with the terms and conditions of this Lease, or in connection with insurance policies which they obtain insuring such insurable interest as Landlord or Tenant may have in its own properties, whether personal or real, shall expressly waive any right of subrogation on the part of the insurer against the Landlord or Tenant. Landlord and Tenant each waives all right of recovery against the other, its agents or employees for any loss, damage or injury of any nature whatsoever to property or person for which the waiving party is required by this Lease to carry insurance.

 

9. SIGNS

Landlord will provide a sign monument listing all of the tenants in the Building. At its sole expense the Tenant shall have the right to install on the interior doors at the Leased Premises, only such signs as are required by Tenant for the purpose of identifying the Tenant.

 

10. ASSIGNMENT AND SUBLETTING

10.1 The Tenant may not assign or sublet the Leased Premises without Landlord’s consent, which shall not be unreasonably withheld. Tenant shall advise the Landlord in writing, by certified mail, return receipt requested of its desire to assign or sublease and Landlord shall have 60 days from receipt of such notice to notify Tenant whether it rejects or consents to the assignment or sublease. Landlord shall also have the option to elect to re-capture the Leased Premises and terminate the Lease, if and only if Tenant desires to sublease all of the Leased Premises for the entire term. If Landlord elects to recapture the Leased Premises, Tenant shall surrender the Leased Premises no later than 90 days after Landlord’s written notice of its election to recapture.

10.2 The Landlord’s consent shall not be required and the terms and conditions of Paragraph 10.1 shall not apply as to Landlord’s right to recapture if the Tenant assigns or subleases the Leased Premises to a parent, subsidiary, affiliate or a company into which Tenant is merged or with which Tenant is consolidated, or to the purchaser of all or substantially all of the assets of Tenant.

10.3 In connection with any permitted assignment or subletting, (i) the Tenant shall pay monthly to the Landlord 50% of any increment in rent (net of any reasonable broker’s commissions, attorney’s fees and marketing costs incurred by Tenant in connection therewith) received by Tenant per square foot over the Base Rent then in effect during the year of the assignment or subletting, which payment shall be made monthly together with the required rent hereunder; and (ii) if Tenant receives any

 

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consideration or value for such assignment or subletting, Landlord shall be paid  50%  of any such consideration or value within 10 days after receipt of the same by Tenant. As a condition hereunder, Tenant covenants with Landlord that it will furnish to Landlord a copy of all pertinent documents with respect to any such assignment or subletting so as to establish Tenant’s obligation to Landlord hereunder.

10.4 In the event of any assignment or subletting permitted by the Landlord, the Tenant shall remain and be directly and primarily responsible for payment and performance of the within Lease obligations, and the Landlord reserves the right, at all times, to require and demand that the Tenant pay and perform the terms and conditions of this Lease. In the case of a complete recapture, Tenant shall be released from all further liability with respect to the recaptured space. No such assignment or subletting shall be made to any tenant who shall occupy the Leased Premises for any use other than that which is permitted to the Tenant, or which would in any way violate applicable laws, ordinances or rules and regulations of governmental boards and bodies having jurisdiction.

 

11. FIRE AND CASUALTY

11.1 In case of any damage to or destruction of any portion of the building of which the Leased Premises is a part by fire or other casualty occurring during the term of this Lease (or previous thereto), which shall render at least 1/3 of the floor area of the Leased Premises or the building untenantable or unfit for occupancy, which damage cannot be repaired within 180 days from the happening of such casualty, using reasonable diligence (“Total Destruction”) then the term hereby created shall, at the option of the Landlord or Tenant, upon written notice to the Tenant or Landlord, as the case may be, within 15 days of such fire or casualty, cease and become null and void from the date of such Total Destruction. In such event the Tenant shall immediately surrender the Leased Premises to the Landlord and this Lease shall terminate. The Tenant shall only pay rent to the time of such Total Destruction. However, in the event of Total Destruction if the Landlord shall elect not to cancel this Lease within the 15 day period the Landlord shall repair and restore the same to substantially the same condition as it was prior to the damage or destruction, with reasonable speed and dispatch. The rent shall not be accrued after said damage or while the repairs and restorations are being made, but shall recommence immediately after the premises are Substantially Complete as defined in paragraph 3.6. In any case where Landlord must restore, consideration shall be given for delays under the Force Majeure paragraph in this Lease. Whether or not this Lease has been terminated as a result of a casualty, in every instance, all insurance proceeds payable as a result of damage or destruction to the Building shall be paid to Landlord as its sole and exclusive property.

11.2 In the event of any other casualty which shall not be tantamount to Total Destruction the Landlord shall repair and restore the Building and the Leased Premises to substantially the same condition as they were prior to the damage or destruction, with reasonable speed and dispatch. The rent shall abate or shall be equitably apportioned as to any portion of the Leased Premises which shall be unfit for occupancy by the Tenant, or which cannot be used by the Tenant to conduct its business. The rent shall recommence immediately after the Leased Premises are Substantially Complete as defined in paragraph 3.6.

11.3 In the event of any casualty caused by an event which is not covered by Landlord’s insurance policy, the Landlord may elect to treat the casualty as though it had insurance or it may terminate the Lease. If it treats the casualty as though it had insurance then the provisions of this paragraph shall apply. The Landlord shall serve a written notice upon the Tenant within 15 days of the casualty specifying the election which it chooses to make.

11.4 In the event the Landlord rebuilds, the Tenant agrees, at its cost and expense, to forthwith remove any and all of its equipment, fixtures, stock and personal property in order to permit Landlord to expedite the construction. The Tenant shall assume at its sole risk the responsibility for damage to or security of such fixtures and equipment in the event that any portion of the building area has been damaged and is not secure.

 

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12. COMPLIANCE WITH LAWS, RULES AND REGULATIONS

 

  12.1 (a) The Tenant agrees that upon acceptance and occupancy of the Leased Premises, it will, at its own cost and expense, comply with all statutes, ordinances, rules, orders, regulations and requirements of the Federal, State and Municipal governments arising from the operations of Tenant at the Leased Premises. The Tenant also agrees that it will not commit any nuisance or excessive noise, and will dispose of all garbage and waste in connection with its operations so as to avoid unreasonable emissions of dirt, fumes, odors or debris.

(b) The Tenant agrees, at its own cost and expense, to comply with such regulations or requests as may be required by the fire or liability insurance carriers providing insurance for the Leased Premises, and the Board of Fire Underwriters, in connection with Tenant’s use and occupancy of the Leased Premises.

12.2 In case the Tenant shall fail to comply with all material provisions of the aforesaid statutes, ordinances, rules, orders, regulations and requirements then the Landlord may, after 10 days’ notice (except for emergency repairs, which may be made immediately), enter the Leased Premises and take any reasonable actions to comply with them, at the cost and expense of the Tenant, unless the Tenant is diligently pursuing the correction of the problem. The cost thereof shall be added to the next month’s rent and shall be due and payable as such, or the Landlord may deduct the same from the balance of any sum remaining in the Landlord’s hands. This provision is in addition to the right of the Landlord to terminate this Lease under the provisions of paragraph 14.2. However, in the event that all necessary repairs are made by Tenant, the initial failure to comply with the aforesaid laws and regulations shall not constitute an event of default.

12.3 Tenant expressly covenants and agrees to indemnify, defend and save the Landlord harmless against any claim, damage, liability, cost, penalties, or fines which the Landlord may suffer as a result of air, ground or water pollution caused by the Tenant in its use of the Leased Premises. The Tenant covenants and agrees to notify the Landlord immediately of any claim or notice served upon it with respect to any claim that the Tenant is causing air, ground or water pollution; and the Tenant shall take immediate steps to halt, remedy or cure any pollution of air, ground or water caused by the Tenant by its use of the Leased Premises.

12.4 Tenant expressly covenants and agrees to fully comply with the provisions of the New Jersey Industrial Site Recovery Act (N.J.S.A. I3:lK-6, et seq.) “ISRA”, and its regulations, prior to the termination of the Lease or at any time that any action of the Tenant triggers the applicability of ISRA. In particular, the Tenant agrees that it shall comply with the provisions of ISRA in the event of any “closing, terminating or transferring” of Tenant’s operations, as defined by and in accordance with the regulations. In the event evidence of such compliance is not delivered to the Landlord prior to surrender of the Leased Premises by the Tenant to the Landlord, it is understood and agreed that the Tenant shall be liable to pay to the Landlord an amount equal to two times the Base Rent then in effect, together with all applicable Additional Rent from the date of such surrender until such time as evidence of compliance with ISRA has been delivered to the Landlord, and together with any costs and expenses incurred by Landlord in enforcing Tenant’s obligations under this paragraph. Evidence of compliance, as used herein, shall mean a “letter of non-applicability” issued by the New Jersey Department of Environmental Protection (“NJDEP”), an approved “negative declaration”   or a “remediation action plan” which has been fully implemented and approved by NJDEP, or other equivalent document as may then be prescribed by applicable regulations. Evidence of compliance shall be delivered to the Landlord, together with copies of all submissions made to the NJDEP, including all environmental reports, test results and other supporting documentation. In addition to the above, Tenant agrees that it shall cooperate with Landlord in the event ISRA is applicable to any portion of the property of which the Leased Premises are a part. In such case, Tenant agrees that it shall fully cooperate with Landlord in connection with any information or documentation which may be requested by the NJDEP. In the event that any remediation of the Property is required in connection with the conduct by Tenant of its business at the Leased Premises, Tenant expressly covenants and agrees that it shall be responsible for that portion of the remediation which is attributable to the

 

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Tenant’s operation. Tenant hereby represents and warrants that its Standard Industrial Classification No. is 8731, and that Tenant shall not generate, manufacture, refine, transport, treat, store, handle or dispose of “hazardous substances” as the same are defined under ISRA and the regulations promulgated pursuant thereto, except in strict compliance with all governmental rules, regulations and procedures. Tenant hereby agrees that it shall promptly inform Landlord of any change in its SIC number and obtain Landlord’s consent for any change in the nature of the business to be conducted in the Leased Premises. The within covenants shall survive the expiration or earlier termination of the lease term.

 

13. INSPECTION BY LANDLORD

13.1 The Tenant agrees that the Landlord shall have the right to enter into the Leased Premises at all reasonable hours for the purpose of examining the same upon reasonable advance notice of not less than 24 hours (except in the event of emergency), or to make such repairs as are necessary. Any repair shall not unduly interfere with Tenant’s use of the Leased Premises and Landlord agrees to comply with Tenant’s reasonable requirements with regard to access to any sensitive areas.

 

14. DEFAULT BY TENANT

14.1 Each of the following shall be deemed a default by Tenant and a breach of this Lease:

 

  (a) (1) filing of a petition by the Tenant for adjudication as a bankrupt, or for reorganization, or for an arrangement under any federal or state statute, except in a Chapter 11 Bankruptcy where the rent and Additional Rent stipulated herein is being paid and the terms of the Lease are being complied with;

(2) dissolution or liquidation of the Tenant;

(3) appointment of a permanent receiver or a permanent trustee of all or substantially all of the property of the Tenant, if such appointment shall not be vacated within 60 days, provided the rent and Additional Rent stipulated herein is being paid and the terms of the Lease are being complied with, during said 60 day period;

(4) taking possession of the property of the Tenant by a governmental officer or agency pursuant to statutory authority for dissolution, rehabilitation, reorganization or liquidation of the Tenant if such taking of possession shall not be vacated within 60 days, provided the rent and Additional Rent stipulated herein is being paid and the terms of the Lease are being complied with, during said 60 day period;

(5) making by the Tenant of an assignment for the benefit of creditors;

(6) abandonment, desertion or vacation of the Leased Premises by the Tenant; and

(7) failure of the Tenant to move into or take possession of the Leased Premises within 15 days of the Commencement Date.

(b) Default in the payment of the rent or Additional Rent herein reserved or any part thereof, which continues for 10 days.

(c) A default in the performance of any other covenant or condition which this Lease requires the Tenant to perform, for a period of 15 days after notice. However, no default on the part of Tenant shall be deemed to exist if it diligently commences efforts to rectify same and Landlord is indemnified against loss or liability arising from the default.

14.2 In the event of any default set forth above and the lapse of any applicable grace period, Landlord may serve written notice upon the Tenant electing to terminate this Lease upon a specified date not less than 10 days after the date of serving such notice and this Lease shall then expire on the date so specified as if that date had been originally fixed as the expiration date of the term herein granted.

 

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14.3 In case this Lease shall be terminated due to Tenant’s default as set forth above, Landlord or its agents may, immediately or any time thereafter, re-enter and resume possession of the Leased Premises or such part thereof, and remove all persons and property therefrom, either by summary proceedings or a suitable action or proceeding at law, without being liable for any damages therefor. No re-entry by Landlord shall be deemed an acceptance of a surrender of this Lease. However, if the Tenant is in default and moves out, or is dispossessed, and fails to remove any property, machinery, equipment and fixtures or other property within 10 days of the date Landlord sends a written notice to the last known address of the Tenant, then the property, machinery, equipment and fixtures or other property left at the Leased Premises shall, at the option of the Landlord, be conclusively presumed to be abandoned and maybe disposed of by the Landlord without accounting to Tenant for any of the proceeds, or the Landlord may remove such property and charge the reasonable cost and expense of removal and storage to the Tenant before disposing of such property. The Tenant shall be liable for any damage which it causes in the removal of said property from the Leased Premises.

14.4 In case this Lease shall be terminated, due to Tenant’s default as set forth above Landlord may relet the whole or any portion of the Leased Premises for any period equal to or greater or less than the remainder of the then current term, for any sum which it may deem reasonable, to any tenant which it may deem suitable and satisfactory, and for any use and purpose which it may deem appropriate. In connection with any such lease Landlord may make such changes in the character of the improvements on the Leased Premises as Landlord may determine to be appropriate or helpful in effecting such lease and may grant concessions or free rent. Landlord shall make reasonable efforts to relet the Leased Premises. Landlord shall not in any event be required to pay Tenant any sums received by Landlord on such reletting of the Leased Premises.

14.5 In the event this Lease is terminated due to Tenant’s default as set forth above, and whether or not the Leased Premises be relet, Landlord shall be entitled to recover from the Tenant all rent due and all expenses, including reasonable counsel fees, incurred by Landlord in recovering possession of the Leased Premises, and all reasonable costs and charges for the care of the Leased Premises while vacant, which damages shall be due at such time as they are incurred by Landlord; and all other damages set forth in this Paragraph 14 and in Paragraph 15. Without any previous notice or demand, separate actions may be maintained by Landlord against Tenant from time to time to recover any damages which have become due and payable to the Landlord without waiting until the end of the term.

 

15. LIABILITY OF TENANT FOR DEFICIENCY

In the event that the relation of the Landlord and Tenant terminates by reason of any default set forth in paragraph 14, and the Landlord reenters the Property as permitted herein, it is hereby agreed that the Tenant shall remain liable to pay in monthly payments the Rent and any other charges which shall accrue. The Tenant expressly agrees to pay as Landlord’s damages for such breach of this Lease the difference between the Rent herein and the rent received, if any, by the Landlord, during the remainder of the unexpired term.

 

16. NOTICES

All notices required by this Lease shall be given either by certified mail, return receipt requested, or overnight courier, or personal delivery with receipt, at the address set forth on the first page of this Lease, and/or such other place as the parties may designate in writing.

 

17. NON-WAIVER BY EITHER PARTY

The failure of either party to insist upon the strict performance of any of the terms of this Lease, or to exercise any option contained herein, shall not be construed as a waiver of any such term. Acceptance by either party of the performance of anything required by this Lease to be performed, with the knowledge of the breach of any term of this Lease, shall not be deemed a waiver of such breach,

 

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nor shall acceptance of Rent by Landlord in a lesser amount than is due (regardless of any endorsement on any check, or any statement in any letter accompanying any payment of Rent) be construed either as an accord and satisfaction or in any manner other than as payment on account of the earliest rent then unpaid by Tenant. No waiver by either party of any term of this Lease shall be deemed to have been made unless expressed in writing and signed by that party.

 

18. RIGHT OF TENANT TO MAKE ALTERATIONS AND IMPROVEMENTS

The Tenant may not make alterations, additions or improvements to the Leased Premises, or change the door locks or window coverings, or in any way alter access to the Leased Premises (“Alterations”) without the consent of the Landlord, which consent shall not be unreasonably withheld. Landlord agrees to review any Alterations proposed by Tenant within 15 days of receipt of plans and specifications, and advise Tenant whether such Alterations are permissible and whether Tenant will be required to remove such Alterations at the conclusion of the Lease term. Tenant shall be permitted to make cosmetic or decorative changes to the Leased Premises, such as painting, wallpaper or carpeting. Any approval given is not intended to subject the Landlord’s property to liability under any lien law. Tenant shall be responsible for obtaining at its own cost and expense all licenses, permits and approvals that may be required by any governmental entity having jurisdiction over the approved alterations, additions and/or improvements. Tenant shall furnish to Landlord as-built drawings of any alterations, additions or improvements which are made.

 

19. NON-LIABILITY OF LANDLORD

Tenant agrees to assume all risk of damage to its property, equipment and fixtures occurring in or about the Leased Premises, whatever the cause of such damage or casualty. Landlord shall not be liable for any damage or injury to property or person caused by or resulting from steam, electricity, gas, water, rain, ice or snow, or any leak or flow from or into any part of the building, or from any damage or injury resulting or arising from any other cause or happening whatsoever.

 

20. RESERVATION OF EASEMENT

Landlord reserves the right, easement and privilege to enter on the Leased Premises in order to install, at its own cost and expense, any utility lines and services in connection therewith as may be required by the Landlord. It is understood and agreed that if such work as may be required by Landlord requires any interior installation, or displaces any exterior paving or landscaping, the Landlord shall at its own cost and expense, restore such items, to substantially the same condition as they were before such work. The Landlord covenants that the foregoing work shall not unreasonably interfere with the normal operation of Tenant’s business.

 

21. STATEMENT OF ACCEPTANCE

Upon the delivery of the Leased Premises to the Tenant the Tenant covenants and agrees that it will furnish to Landlord a statement which shall set forth the Date of Commencement and the Date of Expiration of the lease term,

 

22. FORCE MAJEURE

Except for the obligation of the Tenant to pay Rent and other charges, the period of time during which the Landlord or Tenant is prevented from performing any act required to be performed under this Lease by reason of fire, catastrophe, strikes, lockouts, civil commotion, weather conditions, acts of God, government prohibitions or prescriptions or embargoes, inability to obtain material or labor by reason of governmental regulations, the act or default of the other party, or other events beyond the reasonable control of Landlord or Tenant, as the case may be, shall be added to the time for performance of such act.

 

23. STATEMENTS BY LANDLORD AND TENANT

Landlord and Tenant agree at any time and from time to time upon not less than 5 days’ prior notice from the other to execute, acknowledge and deliver to the party requesting same, a statement in writing, certifying that this Lease is unmodified and in full force and effect (or if there have been modifications, that the same is in full force and effect as modified and stating the modifications), that it is not in default (or if claimed to be in default, stating the amount and nature of the default) and specifying the dates to which the Rent and other charges have been paid in advance.

 

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24. CONDEMNATION

24.1 If due to condemnation, (i) more than 15% of the Leased Premises is taken or rendered untenantable, or (ii) more than 25% of the ground is taken (including parking areas, but excluding front, side and rear set back areas) and, in Landlord’s opinion, said taking unreasonably or unduly interferes with the use of the Leased Premises, the lease term created shall terminate from the date when the authority exercising the power of eminent domain takes or interferes with the use of the Property. The Tenant shall be responsible for the payment of Rent until the time of surrender. In any event, no part of the Landlord’s condemnation award shall be claimed by the Tenant. Without diminishing Landlord’s award, the Tenant shall have the right to make a claim against the condemning authority for such independent claim which it may have, including without limit, Tenant Improvements made or paid for by Tenant.

24.2 In the event of any partial taking which would not be cause for termination of the Lease, or in the event of any taking in excess of the percentages provided above and Tenant retains the balance of the Leased Premises remaining after such taking, then the Rent shall abate in an amount to be mutually agreed upon between the Landlord and Tenant based on the relationship that the character of the property prior to the taking bears to the property which shall remain after the condemnation. The Landlord shall, to the extent permitted by applicable law and as the same may be practicable, promptly make such repairs and alterations in order to restore the Building and/or improvements to a usable condition to the extent of any condemnation award received by Landlord.

 

25. LANDLORD’S REMEDIES

25.1 The rights and remedies given to the Landlord in this Lease are distinct, separate and cumulative remedies, and no one of them, whether or not exercised by the Landlord, shall be deemed to be in exclusion of any of the others.

25.2 In addition to any other legal remedies for violation or breach of this Lease by the Tenant or by anyone holding or claiming under the Tenant such violation or breach shall be restrainable by injunction at the suit of the Landlord.

25.3 No receipt of money by the Landlord from any receiver, trustee or custodian or debtors in possession shall reinstate, or extend the term of this Lease or affect any notice theretofore given to the Tenant, or to any such receiver, trustee, custodian or debtor in possession, or operate as a waiver or estoppel of the right of the Landlord to recover possession of the Leased Premises for any of the causes therein enumerated by any lawful remedy; and the failure of the Landlord to enforce any covenant or condition by reason of its breach by the Tenant shall not be deemed to void or affect the right of the Landlord to enforce the same covenant or condition on the occasion of any subsequent default or breach.

 

26. QUIET ENJOYMENT

The Landlord covenants that the Tenant, on paying the Rent and performing the covenants and conditions contained in this Lease, may peaceably and quietly have, hold and enjoy the Leased Premises, in the manner of a multi-tenanted building, for the Lease term.

 

27. SURRENDER OF PREMISES

On the last day, or earlier permitted termination of the Lease, Tenant shall quit and surrender the Leased Premises in good and orderly condition and repair (reasonable wear and tear, and damage by fire or other casualty excepted) and shall deliver and surrender the Leased Premises to the Landlord peaceably, together with all Tenant Improvements. The Landlord reserves the right, however, to require the Tenant at its cost and expense to remove any Alterations installed by the Tenant, and restore the Leased Premises to its original state, normal wear and tear excepted, unless Landlord has previously consented to allow such Alterations to remain. Prior to

 

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the expiration of the Lease term the Tenant shall remove all of its tangible property, fixtures and equipment from the Leased Premises. All property not removed by Tenant shall be deemed abandoned by Tenant, and Landlord reserves the right to charge the reasonable cost of such removal and disposal to the Tenant. If the Leased Premises are not surrendered at the end of the Lease term, the Tenant shall be liable for double rent under  NJSA  2A:42-6, and Tenant shall indemnify Landlord against loss or liability resulting from delay by Tenant in surrendering the Leased Premises, including, without limitation any claims made by any succeeding tenant founded on the delay, and any loss of income suffered by Landlord. These covenants shall survive the termination of the Lease.

 

28. INDEMNITY

Anything in this Lease to the contrary notwithstanding, and without limiting the Tenant’s obligation to provide insurance hereunder, the Tenant covenants and agrees that it will indemnify, defend and save harmless the Landlord against and from all liabilities, obligations, damages, penalties, claims, costs, charges and expenses, including without limitation reasonable attorneys’ fees, which may be imposed upon or incurred by Landlord by reason of any of the following occurring during the term of this Lease:

(a) Any matter, cause or thing arising out of Tenant’s use, occupancy, control or management of the Leased Premises and any part thereof.

(b) Any negligence on the part of the Tenant or any of its agents, employees, licensees or invitees, arising in or about the Leased Premises.

(c) Any failure on the part of Tenant to perform or comply with any of its covenants, agreements, terms or conditions contained in this Lease.

Landlord shall promptly notify Tenant of any such claim asserted against it and shall promptly send to Tenant copies of all papers or legal process served upon it in connection with any action or proceeding brought against Landlord.

 

29. BIND AND CONSTRUE CLAUSE

The terms, covenants and conditions of this Lease shall be binding upon, and inure to the benefit of, each of the parties hereto and their respective heirs, successors and assigns. If any one of the provisions of this Lease shall be held to be invalid by a court of competent jurisdiction, such adjudication shall not affect the validity or enforceability of the remaining portions of this Lease. The parties each acknowledge to the other that this Lease has been drafted by both parties, after consultation with their attorneys, and in the event of any dispute, the provisions are not to be interpreted against either party as the drafter of the Lease.

 

30. INCLUSIONS

The neuter gender when used herein, shall include all persons and corporations, and words used in the singular shall include words in the plural where the text of the instrument so requires.

 

31. DEFINITION OF TERM “LANDLORD”

When the term “Landlord” is used in this Lease it shall be construed to mean and include only the entity which is the owner of title to the building. Upon the transfer by the Landlord of the title, the Landlord shall advise the Tenant in writing by certified mail, return receipt requested, of the name of the Landlord’s transferee. In such event, the Landlord shall be automatically freed and relieved from and after the date of such transfer of title of all personal liability with respect to the performance of any of the covenants and obligations on the part of the Landlord herein contained to be performed, provided any such transfer and conveyance by the Landlord is expressly subject to the assumption by the transferee of the obligations of the Landlord hereunder.

 

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32. COVENANTS OF FURTHER ASSURANCES

If, in connection with obtaining financing for the improvements on the Leased Premises, the mortgage lender shall request reasonable modifications in this Lease as a condition to such financing, Tenant will not unreasonably withhold, delay or refuse its consent thereto, provided that such modifications do not in Tenant’s reasonable judgment increase the obligations of Tenant hereunder or materially adversely affect the leasehold interest hereby created or Tenant’s use and enjoyment of the Leased Premises.

 

33. COVENANT AGAINST LIENS

Tenant agrees that it shall not encumber, or permit to be encumbered, the Leased Premises or the fee thereof by any lien, charge or encumbrance, and Tenant shall have no authority to mortgage or hypothecate this Lease in any way whatsoever. Any violation of this Paragraph shall be considered a breach of this Lease.

 

34. SUBORDINATION

This Lease shall be subject and subordinate at all times to the lien of any mortgages or ground leases or other encumbrances now or hereafter placed on the land, Building and Leased Premises without the necessity of any further instrument or act on the part of Tenant to effectuate such subordination. However, Tenant agrees to execute such further documents evidencing the subordination of the Lease to the lien of any mortgage or ground lease as shall be desired by Landlord within 5 days, provided Landlord’s mortgagee agrees to a non-disturbance agreement.

 

35. EXCULPATION OF LANDLORD

Neither Landlord nor its principals shall have any personal obligation for the payment of any indebtedness or for the performance of any obligation under this Lease. The performance of Landlord’s obligations expressed herein may be enforced only against the Building and land of which the Leased Premises are a part, and the rents, issues and profits thereof. The Tenant agrees that no deficiency judgment or other judgment for money damages shall be entered by it against the Landlord or its principals personally in any action.

 

36. NET RENT

It is the intent of the Landlord and Tenant that this Lease shall yield, net to Landlord, the Base Rent specified and all Additional Rent and charges in each month during the term of the Lease, and that all costs, expenses and obligations of every kind relating to the Leased Premises shall be paid by the Tenant, unless expressly assumed by the Landlord.

 

37. SECURITY

Tenant shall not be required to pay any security deposit.

 

38. BROKERAGE

The parties mutually represent to each other that Julian J. Studley, Inc. is the broker who negotiated and consummated the within transaction, and that neither party dealt with any other broker in connection with the Lease. In the event either party violates this representation, it shall indemnify and defend and hold the other party harmless from all claims and damages. It is agreed that the Landlord shall be responsible, at its sole cost and expense, to pay the brokerage commission in connection with this Lease.

 

39. LATE CHARGES

In addition to any other remedy, a late charge of 1  1 / 2 % per month, retroactive to the date any Rent or payment for Tenant Improvements was due, shall be payable, without notice from Landlord, on any such charges not paid within 5 days of the due date.

 

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40. PRESS RELEASES

Subject to the prior written approval of Tenant (which shall not be unreasonably withheld), Landlord shall have the right to announce the execution of this Lease, the parties hereto, and the real estate brokers involved in such press releases as Landlord shall deem advisable. In addition, Tenant shall permit Landlord to use its name and photographs of the Leased Premises (all photographs being subject to Tenant’s prior consent) in Landlord’s marketing brochures and materials, and Tenant agrees to reasonably cooperate with Landlord in such regard, but at no cost or expense to Tenant.

 

41. WAIVER OF JURY TRIAL

Landlord and Tenant both irrevocably waive a trial by jury in any action or proceeding between them or their successors or assigns arising out of this Lease or any of its provisions, or Tenant’s use or occupancy of the Leased Premises.

 

42. LAWS OF NEW JERSEY

Without regard to principles of conflicts of laws, the validity, interpretation, performance and enforcement of this Lease shall be governed by and construed in accordance with the laws of the State of New Jersey. The sole and exclusive venue for any dispute between the parties shall be in Middlesex County, New Jersey.

 

43. OPTION TO RENEW

Provided the Tenant is not then in default hereunder, it has the right to renew the Lease, for two additional terms of 5 years each, to commence at the end of the prior term of this Lease. The renewal shall be upon the same terms and conditions as contained in this Lease, except that the Base Rent for the option term shall increase by 15% over the Base Rent for the year prior to the year in which the option term commences. The option of the Tenant to renew this Lease is expressly conditioned upon the Tenant delivering to the Landlord a notice, in writing, by certified mail, return receipt requested at least 180 days prior to the date fixed for termination of the then existing Lease term.

 

44. RIGHT OF FIRST OFFER

During the term of this Lease Agreement, Tenant may notify Landlord in writing if it desires to lease specific units in the Building which are in close proximity to the Leased Premises and leased to other tenants (“Designated Units”). Landlord shall first offer to Tenant any Designated Units that become vacant or that Landlord knows will become vacant as of a certain date. Tenant shall then have 5 days after receipt of Landlord’s offer to notify Landlord whether it is interested in leasing such space. If Tenant does not respond during said 5 day period, then Landlord shall be free to market the space to other tenants. If Tenant notifies Landlord, in writing, that it desires to lease said space then the parties agree to negotiate in good faith to reach an agreement on the terms of the lease. In the event the parties have not entered into a lease after a 30 day period, Landlord shall be free to market the space to other tenants.

 

45. CROSS DEFAULT

Landlord and Tenant have entered into another lease at Eastpark at 8A for all of Building #3, in addition to this Lease. Any default, monetary or otherwise, in either lease shall give the Landlord the option to declare a default under both Leases. In the event of such a default, and exercise of this right by Landlord, it shall have all the rights set forth in either Lease.

IN WITNESS WHEREOF, the parties hereto have executed this document on the date first above written.

 

East Park at 8A

/s/    A. Joseph Stern, Partner

Pharmacopeia, Inc.

/s/    Joseph A. Mollica

 

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Exhibit “B”

Payments for Tenant Improvements

The following shall form the basis for the payments for the tenant improvements referred to in the Lease Agreement:

 

  1. Upon execution of the Lease, Tenant shall pay to Landlord the mobilization fee contained in the Preliminary Estimate of Tenant Improvement Costs made part of this Exhibit.

 

  2. Landlord shall thereafter invoice Tenant on Mondays on a biweekly basis with payment for that invoice due on Friday of that same week.

 

  3. All payments shall be based upon the approved Construction Budget pursuant to paragraph 3.2a of the Lease Agreement. Until the approval of the Construction Budget all payments shall be made based upon the Preliminary Estimate of Tenant Improvement Costs contained in this Exhibit B. Any adjustments required to the payments made prior to the issue of the Construction Budget shall be made within five (5) business days of the approval of the Construction Budget.

 

  4. Landlord shall use the standard AIA form as the method of invoicing. Payments made for deposits, materials stored and work performed shall be contained in this shall and shall be paid as described in item 2 above.

 

  5. No retention shall be held by Tenant.

 

  6. Upon Substantial Completion of the Tenant Improvements, full payment of the remaining construction costs shall be made by the Tenant, in accordance with this Lease Agreement.

 

  7. Landlord shall proceed with any “punch list” work required and shall complete this work in accordance with the terms of this Lease Agreement.

 

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Exhibit 10.329

LEASE AGREEMENT

BY AND BETWEEN:

Eastpark at 8A

“Landlord”

- and -

Pharrnacopeia, Inc.

“Tenant”

PREMISES: 3000 Eastpark Boulevard Cranbury, NJ 08512

DATED: August 20, 2003


TABLE OF CONTENTS

 

1.    LEASED PREMISES
2.    TERM OF LEASE
3.    CONSTRUCTION OF THE TENANT IMPROVEMENTS
4.    RENT
5.    PARKING AND USE OF EXTERIOR AREA
6.    USE
7.    REPAIRS AND MAINTENANCE
8.    COMMON AREA EXPENSES. TAXES AND INSURANCE
9.    SIGNS
10.    ASSIGNMENT AND SUBLETTING
11.    FIRE AND CASUALTY
12.    COMPLIANCE WITH LAWS, RULES AND REGULATIONS
13.    INSPECTION BY LANDLORD
14.    DEFAULT BY TENANT
15.    LIABILITY OF TENANT FOR DEFICIENCY
16.    NOTICES
17.    NON-WAIVER BY EITHER PARTY
18.    RIGHT OF TENANT TO MAKE ALTERATIONS AND IMPROVEMENTS
19.    NON-LIABILITY OF LANDLORD
20.    RESERVATION OF EASEMENT
21.    STATEMENT OF ACCEPTANCE
22.    FORCE MAJEURE
23.    STATEMENTS BY LANDLORD AND TENANT
24.    CONDEMNATION
25.    LANDLORD’S REMEDIES
26.    OUIET ENJOYMENT
27.    SURRENDER OF PREMISES
28.    INDEMNITY
29.    BIND AND CONSTRUE CLAUSE
30.    INCLUSIONS
31.    DEFINITION OF TERM “LANDLORD”
32.    COVENANTS OF FURTHER ASSURANCES
33.    COVENANT AGAINST LIENS
34.    SUBORDINATION
35.    EXCULPATION OF LANDLORD
36.    NET RENT
37.    SECURITY
38.    BROKERAGE
39.    LATE CHARGES
40.    PRESS RELEASES
41.    WAIVER OF JURY TRIAL
42.    LAWS OF NEW JERSEY
43.    OPTION TO RENEW
44.    CROSS DEFAULT


AGREEMENT, made August 20, 2003, between Eastpark at 8A, 1000 Eastpark Blvd., Cranbury, New Jersey 08512, “Landlord”; and Pharmacopeia, Inc., 3000 Eastpark Boulevard, Cranbury, NJ 08512, “Tenant”.

WITNESSETH:

WHEREAS, the Landlord intends to lease to the Tenant the entire property known as 3000 Eastpark Boulevard, Cranbury, NJ 08512, (Block 7, Lot 7.03 on the South Brunswick Township Tax Map) (the “Land”) which constitutes a portion of the office/industrial park known as Eastpark at 8A (“Office Park”) together with a building of 58,852 rentable square feet located thereon (“Building” or “Leased Premises”), (the Land and Building shall be referred to together as the “Property”); and

WHEREAS, the parties hereto wish to mutually define their rights, duties and obligations in connection with the Lease;

NOW THEREFORE, in consideration of the promises set forth herein, the Landlord leases unto the Tenant and the Tenant rents from the Landlord the Property, and the Landlord and Tenant do hereby mutually covenant and agree as follows:

 

1. LEASED PREMISES

The Leased Premises shall consist of the entire Building of 58,852 rentable square feet of office and laboratory space, plus an area in the basement of approximately 6,297 rentable square feet, as measured from outside of exterior walls to center line of common walls, together with all improvements to be constructed thereon by the Landlord for the use of the Tenant, and all easements, tenements, appurtenances, hereditaments, rights and privileges appurtenant thereto, and any and all fixtures and equipment which are to be installed by the Landlord for the use of the Tenant in its occupancy of the Leased Premises. Tenant shall also have the right to use all common areas of the Office Park in a similar manner as other Office Park tenants.

 

2. TERM OF LEASE

The term of the Lease shall be 12 years and shall be co-terminus with a lease for Building #1, which is also to be occupied by Tenant. The rent shall commence upon Substantial Completion (as defined hereafter). The 12 year term shall commence on the first day of the month following the date on which Substantial Completion is achieved for both Buildings 1 and 3, and shall expire on the day before the 12th anniversary of the Commencement Date, it being the intent of the parties that the leases for both Buildings shall expire on the same date. The Commencement Date is projected to be January 15, 2004.

 

3. CONSTRUCTION OF THE TENANT IMPROVEMENTS

3.1 The Leased Premises consists of the entire Building currently leased to Tenant. Tenant is taking the Leased Premises in its “as is” condition subject to modifications as shown on the Plans (as hereafter defined) to be prepared by Tenant (“Tenant Improvements”). The Landlord shall provide all necessary labor and materials and perform all the work required to complete the Tenant Improvements. Tenant’s designated representative for all work pertaining to the Tenant Improvements shall be John Harrison and or such other person as is designated in writing by Tenant (“Representative”). The Landlord shall supervise and direct the work on the Tenant Improvements using Landlord’s best skill and attention, and Landlord shall be solely responsible for all construction means, methods, techniques, sequences and procedures and for coordinating all portions of the work on the Tenant Improvements. Landlord warrants to the Tenant that all materials and equipment incorporated in the Tenant Improvements will be new unless otherwise specified, and that all work on the Tenant Improvements will be of good quality, free from known faults and defects, and in substantial conformity with the Plans.

 

  3.2

(a) Landlord shall complete the Tenant Improvements in a good and workmanlike manner and in substantial accordance with plans and specifications (“Plans”) to be prepared by Tenant’s architect, CUH2A. The Plans shall be provided to Landlord on or before September 1, 2003 and shall be in sufficient detail to permit Landlord to apply for a building permit

 

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for the Tenant Improvements (which Landlord shall promptly do), and to prepare a construction budget for the construction of the Tenant Improvements (“Construction Budget”). In the event Tenant does not deliver the Plans to Landlord by the date set forth above, such failure shall not delay the date for the commencement of rent, which shall be presumed to be the projected Commencement Date set forth in paragraph 2. The Construction Budget shall set forth the lump sum amount payable by Tenant to Landlord for the construction of the Tenant Improvements, which amount shall include Landlord’s standard mark-up for general conditions, overhead and profit, which total in the aggregate 20%. The only exception to the lump sum amount shall be the actual fees charged by the Township of South Brunswick for construction permits in connection with the Tenant Improvements, which sums shall be paid by Tenant as set forth hereafter. Landlord shall submit the Construction Budget to Tenant for its approval. Tenant shall give written notice to Landlord within five business days of receipt, as to whether or not the Construction Budget is acceptable. If Tenant does not accept the Construction Budget during such five business day period, then the parties agree to negotiate in good faith to reach an agreement on the Construction Budget. Landlord shall not be obligated to order any equipment or commence work until Tenant has approved the Construction Budget. A complete set of the agreed upon Plans, and the agreed upon Construction Budget, shall be initialed by and distributed to Landlord and Tenant.

(b) Neither the Construction Budget nor the Plans shall be changed or altered in any way except by change order approved in writing by Landlord and Tenant (“Change Order”). All Change Orders shall be valid and binding upon Landlord and Tenant only if authorized by written Change Order signed by Landlord and Tenant’s Representative prior to commencement of the work on the Tenant Improvements reflected thereby. The cost or credit to the Tenant due to any Change Order shall be determined per the terms of such Change Order. In the event the Change Order increases the cost set forth in the Construction Budget, then Landlord shall submit an invoice to Tenant and Tenant shall pay the invoice upon completion of the work or upon the ordering of any equipment, whichever is applicable. The Landlord shall have the right to substitute for the materials and equipment required by the Plans, materials and equipment of equal quality and standard, provided said substitutions conform with applicable building codes and are the subject of a Change Order.

 

  3.3 (a) The Landlord may secure and advance payment for the construction permits and for all other permits and governmental fees, licenses and inspections necessary for the proper execution and completion of the Tenant Improvements. Tenant shall pay such amounts to Landlord not later than 10 business days after receipt of an invoice therefore. Landlord shall not, however, be responsible for securing any environmental or operating permits or certifications which are required in order for Tenant to actually conduct its business.

(b) Tenant shall be responsible for providing Landlord with, and bearing the cost of sufficient copies of the Plans, and sufficient copies of any revisions made to the Plans, in order to obtain the permits and efficiently manage the construction of the Leased Premises. In the event any Change Orders are required during construction, Tenant shall be responsible for all costs related to the preparation and reproduction of plans therefor, unless the Change Order was solely initiated by Landlord, in which case Landlord shall be responsible for such costs. After construction is complete, Tenant shall be responsible for all costs related to the reproduction of “as built” Plans. In all instances where Plans are required, Tenant shall provide Landlord with a reproducible set. Landlord will also be provided with a current plot file containing the Plans at no cost to Landlord. Tenant agrees to have its Architect execute Exhibit “A” affirming Landlord’s right to the Plans.

 

  3.4 (a) Tenant shall pay Landlord directly for the construction costs of Tenant Improvements in accordance with the schedule attached hereto as Exhibit “B”. In the event Tenant fails to pay to Landlord any sum set forth on Exhibit “B” when it is due, Landlord shall not be obligated to commence or continue work on the Tenant Improvements. Such failure to pay shall constitute a default under this Lease, but shall not delay the Commencement Date of this Lease, which shall be

 

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presumed to be the projected Commencement Date set forth in paragraph 2, or any of Tenant’s obligations hereunder including, without limitation, Tenant’s obligation to pay all Rent. In the event that Tenant fails to pay to Landlord the final sum set forth on Exhibit “B”, such failure shall constitute a default under this Lease; and Tenant shall not be permitted to occupy the Leased Premises; and Tenant shall commence payment of all Rent; and Landlord shall be entitled to all rights and remedies available hereunder, at law or in equity, which rights shall be cumulative. All sums so owing to Landlord shall constitute Additional Rent and shall be subject to the imposition of late charges as provided in this Lease.

(b) Apart from extensions of time for delays and extensions of the date for the payment of rent, no payment or allowance of any kind shall be claimed by Tenant, or made to the Landlord as compensation for damages on account of any delay from any cause in the Initial: Landlord completion of the Tenant Improvements, whether such delay be avoidable or unavoidable, anything in this Agreement inconsistent herewith or to the contrary notwithstanding.

3.5 Tenant shall be responsible for the design and installation of its own phone, data and communication systems which systems shall be installed in a manner not to interfere with Landlord’s construction efforts. During construction of Tenant Improvements, a representative of Tenant shall inspect the site no less frequently than once a week and verify and agree that the work in progress has been completed in a manner acceptable to Tenant.

3.6 The Tenant Improvements shall be commenced upon issuance of the building permit by governmental entities having jurisdiction therefor and, subject to authorized adjustments, completion of the Tenant Improvements is estimated to be achieved on or about January 15, 2004. As used herein the term “Substantial Completion” shall mean that the Leased Premises have been built and completed in substantial conformity with the Plans, and a temporary or permanent certificate of occupancy or a temporary or permanent certificate of acceptance (“CO/CA”) has been issued permitting Tenant to use and occupy the Leased Premises, even though minor details, adjustments or punch list items which shall not materially impair Tenant’s use and enjoyment of the Leased Premises may not have been finally completed, but which work Landlord agrees shall be diligently pursued to final completion. Tenant shall allow Landlord and its contractors to enter the Leased Premises during normal working hours after issuance of the CO/CA to complete remaining minor work or punch list items, provided Landlord gives advance notice and makes reasonable efforts not to interfere with Tenant’s operations. It is agreed that for the purpose of this Lease, wherever and whenever the term Substantial Completion is used, it shall not include items of maintenance, service, punch list, or guarantee.

 

4. RENT

4.1 Tenant is currently occupying the Building under an existing lease (“Old Lease”) and shall continue to occupy the space during construction of the Tenant Improvements and pay Landlord the Rent set forth in the Old Lease until Substantial Completion. The Old Lease shall be deemed terminated upon commencement of this Lease as set forth in paragraph 2. Tenant shall pay base rent (“Base Rent”) hereunder as follows:

(a) During the first 4 years of the term, an estimated annual base rent per square foot of $20.58 for all above ground space and $4.00 for the basement space (provided it is only used in its “as is” condition), for an aggregate annual base rent of $l,236,362.16 (“Initial Base Rent”), payable monthly in the sum of $l03,030.l8.

(b) During the second 4 years of the term, the Base Rent shall be increased by adding to the Initial Base Rent the increase in the Consumer Price Index (“CPI”) as follows, and such sum shall be the Base Rent for the second 4 years of the term (the “Adjusted Base Rent”):

The “All Items” Index Figures for the New York-Northeastern New Jersey average of the “Consumer Price Index for All Urban Consumers” (revised CPI-U) (1982-1984 equal to 100) published by the Bureau of Labor Statistics of the U.S. Department of Labor (“Index”) for the month 2 months prior to the date of Substantial Completion shall be compared with

 

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the same index for the month 2 months prior to the beginning month of the second 4 years of the Lease term. If there is an increase in the Index that percentage increase shall be used to determine the rent increase over the original Base Rent, as shown in the following example:

If the Index figure for the month 2 months prior to the date of Substantial Completion is 100 (the denominator) and the Index figure for the month 2 months prior to the beginning of the second 4 years of the lease term is 110, the increase in the Index figures will produce an increase of 10%.

 

  (110-100)    = 10%   
  100      

Applying the formula, 10% of $1,236,362.16 is equal to $123,636.22. Adding that amount to the original Base Rent produces an annual rent for the second 4 years of $1,359,998.38 payable in equal monthly installments of $l13,333.20.

However, in no event shall the increase in rent be more than 12%.

(1) In the event that the Index figure is discontinued the parties shall agree on an equivalent and substituted Cost of Living Index to be applied in the same manner. In the event the parties cannot mutually agree as to a substituted Index, then the issue shall be submitted for arbitration to the American Arbitration Association to take place in South Brunswick or any of its contiguous municipalities, with the cost thereof divided between the parties.

(2) If the base year (1982-84 equal to 100) herein above referred to with respect to the “Index” shall be changed after the execution of the Lease, appropriate adjustments based on such new Index shall be made so as to have a proper application of the Cost of Living formula.

(c) During the third 4 years of the term, the Base Rent shall increase according to the same CPI formula set forth above using the Adjusted Base Rent, but not more than 12 % over the Adjusted Base Rent for the second 4 years.

4.2 In addition to the Base Rent, Tenant shall pay as additional rent (“Additional Rent”) all real estate taxes for the Property, plus its proportionate share of the repairs, maintenance, insurance and any other charges allocated amongst tenants, as more specifically described in paragraph 8 (“Common Area Expenses”), based on the relationship between the rentable square footage leased to Tenant and the rentable square footage of building construction completed and occupied in the Office Park. Tenant’s Common Area Expenses shall be adjusted as of each January 1st during the term based on the increase in Common Area Expenses set forth in paragraph 8.

4.3 The Base Rent and Additional Rent shall be referred to hereafter as “Rent”.

4.4 Tenant covenants to pay the Rent in lawful money of the United States which shall be legal tender for the payment of all debts, public and private, at the time of payment. Such Rent shall be paid to Landlord at its office address hereinabove set forth, or at such other place as Landlord may, from time to time, designate by notice to Tenant.

4.5 Rental payments shall be payable in advance in equal monthly installments on the first day of each calendar month. The Rent shall be payable by Tenant without any set-off or deduction of any kind or nature whatsoever and without notice or demand. The sum of all increases required to be paid as Additional Rent or Base Rent in accordance with this Lease, shall be paid to Landlord within 10 days following the giving of notice hereof by Landlord of such increases.

 

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5. PARKING AND USE OF EXTERIOR AREA

5.1 The Tenant shall have the right to the exclusive use of all parking spaces serving the Property. The Landlord and Tenant mutually agree that they will not block, hinder or otherwise obstruct the access driveways and parking areas so as to impede the free flow of vehicular traffic in the Office Park. In connection with the use of the loading platforms, if any, Tenant agrees that it will not use the same so as to unreasonably interfere with the use of the access driveways and parking areas. Tenant shall not store trailers or other vehicles on any portion of the access driveways or does parking areas, and may not utilize any portion often Property for any other purpose unless consented to in advance by Landlord.

 

6. USE

The Tenant covenants and agrees to use and occupy the Leased Premises only as an office, pilot scale manufacturing facility and laboratory, which use is expressly subject to all applicable zoning ordinances, rules and regulations of any governmental instrumentalities, boards or bureaus having jurisdiction thereof. Tenant’s use of the Leased Premises shall not interfere with the peaceable and quiet use and enjoyment by other tenants at their respective leased premises located in the Office Park, nor shall Tenant’s activities cause Landlord to be in default under its leases with such other tenants.

 

7. REPAIRS AND MAINTENANCE

7.1 Tenant shall generally maintain and repair the Leased Premises, in a good and workmanlike manner, and shall, at the expiration of the term, deliver the Leased Premises in good order and condition, damages by fire or casualty, the elements and ordinary wear and tear excepted. Tenant covenants and agrees that it shall not cause or permit any waste, damage or disfigurement to the Leased Premises, or any overloading of the floors. Tenant shall maintain and make all repairs to the floor surface, plumbing and electrical systems including all ballasts and fluorescent fixtures located within the Leased Premises, and the entire HVAC system. Landlord shall be responsible for repairs necessary to the roof, exterior and load-bearing walls, and electric and plumbing systems to the point where they enter the Leased Premises, unless repair is necessitated by any act of Tenant, or its agents, employees or contractors.

7.2 The Tenant shall, at its own cost and expense, pay all utility meter and service charges, including gas, water and electric servicing the Leased Premises. The Tenant agrees to maintain all leased areas at a minimum temperature of 45 degrees, excluding cold rooms on other rooms specifically designed for a lower temperature, to prevent the freezing of domestic water and sprinkler pipes. Tenant shall not store any items outside the Leased Premises, and shall deliver its garbage and recyclables to the central receiving area on the Property. Tenant shall dispose of all hazardous/medical waste with an approved hauler at its own cost.

7.3 Landlord does not warrant that any services Landlord or any public utilities supply will not be interrupted. Services may be interrupted because of accidents, repairs, alterations, improvements or any other reason beyond the reasonable control of Landlord, not including the gross negligence of Landlord or its agents.

 

8. COMMON AREA EXPENSES. TAXES AND INSURANCE

8.1 The Tenant shall pay to the Landlord, monthly, as Additional Rent its proportionate share of the following items all of which shall be known as Common Area Expenses:

(a) The costs incurred by the Landlord for the operation, maintenance or repair of the following items in the Office Park, (“Operating Costs”):

(1) lawns and landscaping;

(2) standard water usage and standby sprinkler charges;

 

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(3) exterior lighting;

(4) exterior sewer lines;

(5) exterior utility lines;

(6) repair and maintenance of any signs serving the Office Park;

(7) snow removal;

(8) standard garbage disposal and recycling;

(9) general ground maintenance;

(10) parking lot, driveways and walkways;

(11) maintenance contracts for the roof;

(12) pest control;

(13) central station monitoring for fire sprinkler system; and

(14) other ordinary maintenance expenses normally incurred by Landlord relating to the Building and common areas of the Office Park.

Notwithstanding the above, the following items shall be excluded from Common Area Expenses:

(a) Cost of decorating, redecorating, cleaning or other services not provided on a regular basis to the tenants of the Office Park;

(b) Wages, salaries, fees and fringe benefits paid to administrative or executive personnel or officers or partners of Landlord, unless employed at competitive rates as independent contractors at the building or Office Park;

(c) All cost relating to activities for the solicitation, negotiation and execution of leases of space in the Office Park;

(d) Cost of any repair made by Landlord because of the total or partial destruction of the building or the condemnation of a portion of the building;

(e) Any insurance premium for which Landlord is to be reimbursed by Tenant, pursuant to this Lease, or by any other tenant of the Office Park;

(f) Depreciation, interest or rents paid or incurred by Landlord;

(g) Any charge to Landlord for income taxes, franchise taxes or similar taxes:

(h) Collection costs for bad debt expenses not related to Tenant;

(i) Cost of tenant improvements;

(j) Legal, accounting, bank or other fees incurred in connection with any equity or debt financing or sale of the building or Office Park;

 

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(k) Costs of specialized services provided to other tenants but not provided to tenants generally;

(l) Capital expenditures;

(m) Cost to comply with ADA related to the interior of the individual buildings, but not exterior doors or the Office Park;

(n) Costs to cure violations of law or ordinances;

(o) Electric for non-public areas.

(b) The cost of the annual insurance premiums charged to the Landlord for insurance coverage which insure the buildings in the Office Park. The insurance shall be for the full replacement value of all insurable improvements with any customary extensions of coverage including, but not limited to, vandalism, malicious mischief, sprinkler damage and comprehensive liability, and insurance for one year’s rent. The Landlord shall maintain said insurance in effect at all times hereunder. Any increase in the insurance premiums due to a change in rating of the Building which is solely attributable to Tenant’s use, or due to special Tenant equipment, shall be paid entirely by the Tenant. Tenant expressly acknowledges that Landlord shall not maintain insurance on Tenant’s furniture, fixtures, machinery, inventory, equipment or other personal property; and

(c) A management fee of 3% of the Tenant’s Base Rent.

8.2 Within 90 days of the expiration of the first calendar year of the Term, the Landlord shall furnish to Tenant a detailed breakdown of the actual Common Area Expenses. Tenant shall have the right, within 30 days of receipt of the breakdown, and during normal business hours, to examine Landlords books and records with respect to the Common Area Expenses. In the event Tenant’s Proportionate Share shall be greater than the aggregate paid by the Tenant during the prior period, Tenant shall pay any difference, in one lump sum within 30 days after demand. In the event Tenant shall have overpaid its Proportionate Share, any such overage shall be applied to the Base Rent and Additional Rent prospectively due under the Lease. This procedure shall be followed during each year of the lease term, and at the expiration of the Lease, any overage or underage shall be credited or paid after computation by the Landlord, which obligation of Landlord and Tenant shall survive the expiration of the lease term.

8.3 In addition to the payments set forth in Paragraph 8.1, from and after Commencement Date and during the term, Tenant shall pay all real estate taxes and assessments levied by the municipality on the Leased Premises and the Tenant Improvements. Landlord shall immediately forward to Tenant all tax bills received by Landlord, and shall cooperate with Tenant to facilitate the payment of taxes by Tenant. If at any time during the term of this Lease the method or scope of taxation prevailing at the Commencement Date shall be altered, Tenant’s substituted tax or imposition shall be payable and discharged by the Tenant in the manner required pursuant to the law which shall authorize such change. The real estate tax obligation of the Tenant shall include any tax or imposition for parking lot usage which may be levied by any governmental body having jurisdiction thereof. Tenant shall not be obligated to pay any part of (1) any taxes on the income of the Landlord or the holder of an underlying mortgage and any taxes on the income of the lessor under any underlying lease, (2) any corporation, unincorporated business or franchise taxes, (3) any estate, gift, succession or inheritance taxes, (4) any capital gains, mortgage recording or transfer taxes, (5) any taxes or assessments attributable to any sign attached to, or located on, the Building or the land or (6) any similar taxes imposed on the Landlord, the holder of any underlying mortgage or the lessor under any underlying lease.

8.4 Tenant’s Share of Common Area Expenses for any calendar year, part of which falls within the term of this Lease and part of which does not, shall be appropriately prorated.

 

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8.5 If at any time during the term of this Lease the method or scope of taxation prevailing at the commencement of the lease term shall be altered, Tenant’s Proportionate Share of such substituted tax or imposition shall be payable and discharged by the Tenant in the manner required pursuant to the law which shall authorize such change.

8.6 The Tenant covenants and agrees that it will, at its sole cost and expense, carry liability insurance covering the Leased Premises in the minimum amount of $1,000,000.00 per accident for 1 person, $3,000,000.00 per accident for 2 or more persons, and a minimum amount of $300,000.00 for property damage. Tenant shall at all times, carry sufficient insurance to avoid any coinsurance penalties on Tenant’s furniture, furnishings, fixtures, machinery, equipment and installations as well as on any alterations or improvements made to the Leased Premises by Tenant subsequent to the Commencement Date. Such coverage is to include all additions and alterations contemplated hereunder, and shall cover the value of equipment and supplies awaiting installation. The Tenant shall add the Landlord as an additional insured on such policy and will furnish Landlord with a certificate of said liability insurance prior to the Commencement Date and annually thereafter. The certificate shall contain a clause that the policy will not be canceled except on 10 days written notice to the Landlord.

8.7 The parties covenant and agree that the insurance policies required to be furnished in accordance with the terms and conditions of this Lease, or in connection with insurance policies which they obtain insuring such insurable interest as Landlord or Tenant may have in its own properties, whether personal or real, shall expressly waive any right of subrogation on the part of the insurer against the Landlord or Tenant. Landlord and Tenant each waives all right of recovery against the other, its agents or employees for any loss, damage or injury of any nature whatsoever to property or person for which the waiving party is required by this Lease to carry insurance.

 

9. SIGNS

Landlord will provide a sign monument listing all of the tenants in the Building. At its sole expense the Tenant shall have the right to install on the interior doors at the Leased Premises, only such signs as are required by Tenant for the purpose of identifying the Tenant.

 

10. ASSIGNMENT AND SUBLETTING

10.1 The Tenant may not assign or sublet the Leased Premises without Landlord’s consent, which shall not be unreasonably withheld. Tenant shall advise the Landlord in writing, by certified mail, return receipt requested of its desire to assign or sublease and Landlord shall have 45 days from receipt of such notice to notify Tenant whether it rejects or consents to the assignment or sublease. Landlord shall also have the option to elect to re-capture the Leased Premises and terminate the Lease, if and only if Tenant desires to sublease all of the Leased Premises for the entire term. If Landlord elects to recapture the Leased Premises, Tenant shall surrender the Leased Premises no later than 90 days after Landlord’s written notice of its election to recapture.

10.2 The Landlord’s consent shall not be required and the terms and conditions of Paragraph 10.1 shall not apply as to Landlord’s right to recapture if the Tenant assigns or subleases the Leased Premises to a parent, subsidiary, affiliate or a company into which Tenant is merged or with which Tenant is consolidated, or to the purchaser of all or substantially all of the assets of Tenant.

10.3 In connection with any permitted assignment or subletting, (i) the Tenant shall pay monthly to the Landlord 50% of any increment in rent (net of any reasonable broker’s commissions, attorney’s fees and marketing costs incurred by Tenant in connection therewith) received by Tenant per square foot over the Base Rent then in effect during the year of the assignment or subletting, which payment shall be made monthly together with the required rent hereunder; and (ii) if Tenant receives any consideration or value for such assignment or subletting, Landlord shall be paid 50% of any such consideration or value within 10 days after receipt of the same by Tenant. As a condition hereunder, Tenant covenants with Landlord that it will furnish to Landlord a copy of all pertinent documents with respect to any such assignment or subletting so as to establish Tenant’s obligation to Landlord hereunder.

 

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10.4 In the event of any assignment or subletting permitted by the Landlord, the Tenant shall remain and be directly and primarily responsible for payment and performance of the within Lease obligations, and the Landlord reserves the right, at all times, to require and demand that the Tenant pay and perform the terms and conditions of this Lease. In the case of a complete recapture, Tenant shall be released from all further liability with respect to the recaptured space. No such assignment or subletting shall be made to any tenant who shall occupy the Leased Premises for any use other than that which is permitted to the Tenant, or which would in any way violate applicable laws, ordinances or rules and regulations of governmental boards and bodies having jurisdiction.

 

11. FIRE AND CASUALTY

11.1 In case of any damage to or destruction of any portion of the building of which the Leased Premises is a part by fire or other casualty occurring during the term of this Lease (or previous thereto), which shall render at least 1/3 of the floor area of the Leased Premises or the building untenantable or unfit for occupancy, which damage cannot be repaired within 180 days from the happening of such casualty, using reasonable diligence (“Total Destruction”) then the term hereby created shall, at the option of the Landlord or Tenant, upon written notice to the Tenant or Landlord, as the case may be, within 15 days of such fire or casualty, cease and become null and void from the date of such Total Destruction. In such event the Tenant shall immediately surrender the Leased Premises to the Landlord and this Lease shall terminate. The Tenant shall only pay rent to the time of such Total Destruction. However, in the event of Total Destruction if the Landlord shall elect not to cancel this Lease within the 15 day period the Landlord shall repair and restore the same to substantially the same condition as it was prior to the damage or destruction, with reasonable speed and dispatch. The rent shall not be accrued after said damage or while the repairs and restorations are being made, but shall recommence immediately after the premises are Substantially Complete as defined in paragraph 3.6. In any case where Landlord must restore, consideration shall be given for delays under the Force Majeure paragraph in this lease. Whether or not this Lease has been terminated as a result of a casualty, in every instance, all insurance proceeds payable as a result of damage or destruction to the Building shall be paid to Landlord as its sole and exclusive property.

11.2 In the event of any other casualty which shall not be tantamount to Total Destruction the Landlord shall repair and restore the Building and the Leased Premises to substantially the same condition as they were prior to the damage or destruction, with reasonable speed and dispatch. The rent shall abate or shall be equitably apportioned as to any portion of the Leased Premises which shall be unfit for occupancy by the Tenant, or which cannot be used by the Tenant to conduct its business. The rent shall recommence immediately after the Leased Premises are Substantially Complete as defined in paragraph 3.6.

11.3 In the event of any casualty caused by an event which is not covered by Landlord’s insurance policy; the Landlord may elect to treat the casualty as though it had insurance or it may terminate the Lease. If it treats the casualty as though it had insurance then the provisions of this paragraph shall apply. The Landlord shall serve a written notice upon the Tenant within 15 days of the casualty specifying the election which it chooses to make.

11.4 In the event the Landlord rebuilds, the Tenant agrees, at its cost and expense, to forthwith remove any and all of its equipment, fixtures, stock and personal property in order to permit Landlord to expedite the construction. The Tenant shall assume at its sole risk the responsibility for damage to or security of such fixtures and equipment in the event that any portion of the building area has been damaged and is not secure.

 

12. COMPLIANCE WITH LAWS. RULES AND REGULATIONS

12.1 (a) The Tenant agrees that upon acceptance and occupancy of the Leased Premises, it will, at its own cost and expense, comply with all statutes, ordinances, rules, orders, regulations and requirements of the Federal, State and Municipal governments arising from the operations of Tenant at the Leased Premises. The Tenant also agrees that it will not commit any nuisance or excessive noise, and will dispose of all garbage and waste in connection with its operations so as to avoid unreasonable emissions of dirt, fumes, odors or debris.

 

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(b) The Tenant agrees, at its own cost and expense, to comply with such regulations or requests as may be required by the fire or liability insurance carriers providing insurance for the Leased Premises, and the Board of Fire Underwriters, in connection with Tenant’s use and occupancy of the Leased Premises.

12.2 In case the Tenant shall fail to comply with all material provisions of the aforesaid statutes, ordinances, rules, orders, regulations and requirements then the Landlord may, after 10 days’ notice (except for emergency repairs, which may be made immediately), enter the Leased Premises and take any reasonable actions to comply with them, at the cost and expense of the Tenant, unless the Tenant is diligently pursuing the correction of the problem. The cost thereof shall be added to the next month’s rent and shall be due and payable as such, or the Landlord may deduct the same from the balance of any sum remaining in the Landlord’s hands. This provision is in addition to the right of the Landlord to terminate this Lease under the provisions of paragraph However, in the event that all necessary repairs are made by Tenant, the initial failure to comply with the aforesaid laws and regulations shall not constitute an event of default.

12.3 Tenant expressly covenants and agrees to indemnify, defend and save the Landlord harmless against any claim, damage, liability, cost, penalties, or fines which the Landlord may suffer as a result of air, ground or water pollution caused by the Tenant in its use of the Leased Premises. The Tenant covenants and agrees to notify the Landlord immediately of any claim or notice served upon it with respect to any claim that the Tenant is causing air, ground or water pollution; and the Tenant shall take immediate steps to halt, remedy or cure any pollution of air, ground or water caused by the Tenant by its use of the Leased Premises.

12.4 Tenant expressly covenants and agrees to fully comply with the provisions of the New Jersey Industrial Site Recovery Act (N.J.S.A. 13:1K-6, et seq.) “ISRA”, and its regulations, prior to the termination of the Lease or at any time that any action of the Tenant triggers the applicability of ISRA. In particular, the Tenant agrees that it shall comply with the provisions of ISRA in the event of any “closing, terminating or transferring” of Tenant’s operations, as defined by and in accordance with the regulations. In the event evidence of such compliance is not delivered to the Landlord prior to surrender of the Leased Premises by the Tenant to the Landlord, it is understood and agreed that the Tenant shall be liable to pay to the Landlord an amount equal to two times the Base Rent then in effect, together with all applicable Additional Rent from the date of such surrender until such time as evidence of compliance with ISRA has been delivered to the Landlord, and together with any costs and expenses incurred by Landlord in enforcing Tenant’s obligations under this paragraph. Evidence of compliance, as used herein, shall mean a “letter of non applicability” issued by the New Jersey Department of Environmental Protection (“NJDEP”), an approved “negative declaration” or a “remediation action plan” which has been fully implemented and approved by NJDEP, or other equivalent document as may then be prescribed by applicable regulations. Evidence of compliance shall be delivered to the Landlord, together with copies of all submissions made to the NJDEP, including all environmental reports, test results and other supporting documentation. In addition to the above, Tenant agrees that it shall cooperate with Landlord in the event ISRA is applicable to any portion of the property of which the Leased Premises are a part. In such case, Tenant agrees that it shall fully cooperate with Landlord in connection with any information or documentation which may be requested by the NJDEP. In the event that any remediation of the Property is required in connection with the conduct by Tenant of its business at the Leased Premises, Tenant expressly covenants and agrees that it shall be responsible for that portion of the remediation which is attributable to the Tenant’s operation. Tenant hereby represents and warrants that its Standard Industrial Classification No. is 8731, and that Tenant shall not generate, manufacture, refine, transport, treat, store, handle or dispose of “hazardous substances” as the same are defined under ISRA and the regulations promulgated pursuant thereto, except in strict compliance with all governmental rules, regulations and procedures. Tenant hereby agrees that it shall promptly inform Landlord of any change in its SIC number and obtain Landlord’s consent for any change in the nature of the business to be conducted in the Leased Premises. The within covenants shall survive the expiration or earlier termination of the lease term.

 

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13. INSPECTION BY LANDLORD

The Tenant agrees that the Landlord shall have the right to enter into the Leased Premises at all reasonable hours for the purpose of examining the same upon reasonable advance notice of not less than 24 hours (except in the event of emergency), or to make such repairs as are necessary. Any repair shall not unduly interfere with Tenant’s use of the Leased Premises and Landlord agrees to comply with Tenant’s reasonable requirements with regard to access to any sensitive areas.

 

14. DEFAULT BY TENANT

14.1 Each of the following shall be deemed a default by Tenant and a breach of this Lease:

 

  (a) (1) filing of a petition by the Tenant for adjudication as a bankrupt, or for reorganization, or for an arrangement under any federal or state statute, except in a Chapter 11 Bankruptcy where the rent and Additional Rent stipulated herein is being paid and the terms of the Lease are being complied with;

(2) dissolution or liquidation of the Tenant;

(3) appointment of a permanent receiver or a permanent trustee of all or substantially all of the property of the Tenant, if such appointment shall not be vacated within 60 days, provided the rent and Additional Rent stipulated herein is being paid and the terms of the Lease are being complied with, during said 60 day period;

(4) taking possession of the property of the Tenant by a governmental officer or agency pursuant to statutory authority for dissolution, rehabilitation, reorganization or liquidation of the Tenant if such taking of possession shall not be vacated within 60 days, provided the rent and Additional Rent stipulated herein is being paid and the terms of the Lease are being complied with, during said 60 day period;

(5) making by the Tenant of an assignment for the benefit of creditors;

(6) abandonment, desertion or vacation of the Leased Premises by the Tenant; and

(7) failure of the Tenant to move into or take possession of the Leased Premises within 15 days of the Commencement Date.

(b) Default in the payment of the rent or Additional Rent herein reserved or any part thereof, which continues for 10 days.

(c) A default in the performance of any other covenant or condition which this Lease requires the Tenant to perform, for a period of 15 days after notice. However, no default on the part of Tenant shall be deemed to exist if it diligently commences efforts to rectify same and Landlord is indemnified against loss or liability arising from the default.

14.2 In the event of any default set forth above and the lapse of any applicable grace period, Landlord may serve written notice upon the Tenant electing to terminate this Lease upon a specified date not less than 10 days after the date of serving such notice and this Lease shall then expire on the date so specified as if that date had been originally fixed as the expiration date of the term herein granted.

14.3 In case this Lease shall be terminated due to Tenants default as set forth above, Landlord or its agents may, immediately or any time thereafter, re-enter and resume possession of the Leased Premises or such part thereof, it and remove all persons and property therefrom, either by summary proceedings or a suitable action or proceeding at law, without being liable for any damages therefor. No re-entry by Landlord shall be deemed an acceptance of a surrender of this Lease. However, if the Tenant is in default and moves out, or is dispossessed, and fails to remove any property, machinery, equipment and fixtures or other

 

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property within 10 days of the date Landlord sends a written notice to the last known address of the Tenant, then the property, machinery, equipment and fixtures or other property left at the Leased Premises shall, at the option of the Landlord, be conclusively presumed to be abandoned and may be disposed of by the Landlord without accounting to Tenant for any of the proceeds, or the Landlord may remove such property and charge the reasonable cost and expense of removal and storage to the Tenant before disposing of such property. The Tenant shall be liable for any damage which it causes in the removal of said property from the Leased Premises.

14.4 In case this Lease shall be terminated, due to Tenant’s default as set forth above Landlord may relet the whole or any portion of the Leased Premises for any period equal to or greater or less than the remainder of the then current term, for any sum which it may deem reasonable, to any tenant which it may deem suitable and satisfactory, and for any use and purpose which it may deem appropriate. In connection with any such lease Landlord may make such changes in the character of the improvements on the Leased Premises as Landlord may determine to be appropriate or helpful in effecting such lease and may grant concessions or free rent. Landlord shall make reasonable efforts to relet the Leased Premises. Landlord shall not in any event be required to pay Tenant any sums received by Landlord on such reletting of the Leased Premises.

14.5 In the event this Lease is terminated due to Tenant’s default as set forth above, and whether or not the Leased Premises be relet, Landlord shall be entitled to recover from the Tenant all rent due and all expenses, including reasonable counsel fees, incurred by Landlord in recovering possession of the Leased Premises, and all reasonable costs and charges for the care of the Leased Premises while vacant, which damages shall be due at such time as they are incurred by Landlord; and all other damages set forth in this Paragraph 14 and in Paragraph 15. Without any previous notice or demand, separate actions may be maintained by Landlord against Tenant from time to time to recover any damages which have become due and payable to the Landlord without waiting until the end of the term.

 

15. LIABILITY OF TENANT FOR DEFICIENCY

In the event that the relation of the Landlord and Tenant terminates by reason of any default set forth in paragraph 14, and the Landlord reenters the Property as permitted herein, it is hereby agreed that the Tenant shall remain liable to pay in monthly payments the Rent and any other charges which shall accrue. The Tenant expressly agrees to pay as Landlords damages for such breach of this Lease the difference between the Rent herein and the rent received, if any, by the Landlord during the remainder of the unexpired term.

 

16. NOTICES

All notices required by this Lease shall be given either by certified mail, return receipt requested, or overnight courier, or personal delivery with receipt, at the address set forth on the first page of this Lease, and/or such other place as the parties may designate in writing.

 

17. NON-WAIVER BY EITHER PARTY

The failure of either party to insist upon the strict performance of any of the terms of this Lease, or to exercise any option contained herein, shall not be construed as a waiver of any such term. Acceptance by either party of the performance of anything required by this Lease to be performed, with the knowledge of the breach of any term of this Lease, shall not be deemed a waiver of such breach, nor shall acceptance of Rent by Landlord in a lesser amount than is due (regardless of any endorsement on any check, or any statement in any letter accompanying any payment of Rent) be construed either as an accord and satisfaction or in any manner other than as payment on account of the earliest rent then unpaid by Tenant. No waiver by either party of any term of this Lease shall be deemed to have been made unless expressed in writing and signed by that party.

 

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18. RIGHT OF TENANT TO MAKE ALTERATIONS AND IMPROVEMENTS

The Tenant may not make alterations, additions or improvements to the Leased Premises, or change the door locks or window coverings, or in any way alter access to the Leased Premises (“Alterations”) without the consent of the Landlord, which consent shall not be unreasonably withheld. Landlord agrees to review any Alterations proposed by Tenant within 15 days of receipt of plans and specifications, and advise Tenant whether such Alterations are permissible and whether Tenant will be required to remove such Alterations at the conclusion of the Lease term. Tenant shall be permitted to make cosmetic or decorative changes to the Leased Premises, such as painting, wallpaper or carpeting. Any approval given is not intended to subject the Landlord’s property to liability under any lien law. Tenant shall be responsible for obtaining at its own cost and expense all licenses, permits and approvals that may be required by any governmental entity having jurisdiction over the approved alterations, additions and/or improvements. Tenant shall furnish to Landlord as-built drawings of any alterations, additions or improvements which are made.

 

19. NON-LIABILITY OF LANDLORD

Tenant agrees to assume all risk of damage to its property, equipment and fixtures occurring in or about the Leased Premises, whatever the cause of such damage or casualty. Landlord shall not be liable for any damage or injury to property or person caused by or resulting from steam, electricity, gas, water, rain, ice or snow, or any leak or flow from or into any part of the building, or from any damage or injury resulting or arising from any other cause or happening whatsoever.

 

20. RESERVATION OF EASEMENT

Landlord reserves the right, easement and privilege to enter on the Leased Premises in order to install, at its own cost and expense, any utility lines and services in connection therewith as may be required by the Landlord. It is understood and agreed that if such work as may be required by Landlord requires any interior installation, or displaces any exterior paving or landscaping, the Landlord shall at its own cost and expense, restore such items, to substantially the same condition as they were before such work. The Landlord covenants that the foregoing work shall not unreasonably interfere with the normal operation of Tenant’s business.

 

21. STATEMENT OF ACCEPTANCE

Upon the delivery of the Leased Premises to the Tenant the Tenant covenants and agrees that it will furnish to Landlord a statement which shall set forth the Date of Commencement and the Date of Expiration of the lease term.

 

22. FORCE MAJEURE

Except for the obligation of the Tenant to pay Rent and other charges, the period of time during which the Landlord or Tenant is prevented from performing any act required to be performed under this Lease by reason of fire, catastrophe, strikes, lockouts, civil commotion, weather conditions, acts of God, government prohibitions or preemptions or embargoes, inability to obtain material or labor by reason of governmental regulations, the act or default of the other party, or other events beyond the reasonable control of Landlord or Tenant, as the case may be, shall be added to the time for performance of such act.

 

23. STATEMENTS BY LANDLORD AND TENANT

Landlord and Tenant agree at any time and from time to time upon not less than 10 days’ prior notice from the other to execute, acknowledge and deliver to the party requesting same, a statement in writing, certifying that this Lease is unmodified and in full force and effect (or if there have been modifications, that the same is in   full force and effect as modified and stating the modifications), that it is not in default (or if claimed to be in default, stating the amount and nature of the default) and specifying the dates to which the Rent and other charges have been paid in advance.

 

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24. CONDEMNATION

24.1 If due to condemnation, (i) more than 15% of the Leased Premises is taken or rendered untenantable, or (ii) more than 25% of the ground is taken (including parking areas, but excluding front, side and rear set back areas) and, in Landlord’s opinion, said taking unreasonably or unduly interferes with the use of the Leased Premises, the lease term created shall terminate from the date when the authority exercising the power of eminent domain takes or interferes with the use of the Property. The Tenant shall be responsible for the payment of Rent until the time of surrender. In any event, no part of the Landlord’s condemnation award shall be claimed by the Tenant. Without diminishing Landlord’s award, the Tenant shall have the right to make a claim against the condemning authority for such independent claim which it may have, including, without limit, Tenant Improvements made or paid for by Tenant.

24.2 In the event of any partial taking which would not be cause for termination of the Lease, or in the event of any taking in excess of the percentages provided above and Tenant retains the balance of the Leased Premises remaining after such taking, then the Rent shall abate in an amount to be mutually agreed upon between the Landlord and Tenant based on the relationship that the character of the property prior to the taking bears to the property which shall remain after the condemnation. The Landlord shall, to the extent permitted by applicable law and as the same may be practicable, promptly make such repairs and alterations in order to restore the Building and/or improvements to a usable condition to the extent of any condemnation award received by Landlord.

 

25. LANDLORD’S REMEDIES

25.1 The rights and remedies given to the Landlord in this Lease are distinct, separate and cumulative remedies, and no one of them, whether or not exercised by the Landlord, shall be deemed to be in exclusion of any of the others.

25.2 In addition to any other legal remedies for violation or breach of this Lease by the Tenant or by anyone holding or claiming under the Tenant such violation or breach shall be restrainable by injunction at the suit of the Landlord.

25.3 No receipt of money by the Landlord from any receiver, trustee or custodian or debtors in possession shall reinstate, or extend the term of this Lease or affect any notice theretofore given to the Tenant, or to any such receiver, trustee, custodian or debtor in possession, or operate as a waiver or estoppel of the right of the Landlord to recover possession of the Leased Premises for any of the causes therein enumerated by any lawful remedy; and the failure of the Landlord to enforce any covenant or condition by reason of its breach by the Tenant shall not be deemed to void or affect the right of the Landlord to enforce the same covenant or condition on the occasion of any subsequent default or breach.

 

26. QUIET ENJOYMENT

The Landlord covenants that the Tenant, on paying the Rent and performing the covenants and conditions contained in this Lease, may peaceably and quietly have, hold and enjoy the Leased Premises, in the manner of a single-tenanted building, for the Lease term.

 

27. SURRENDER OF PREMISES

On the last day, or earlier permitted termination of the Lease, Tenant shall quit and surrender the Leased Premises in good and orderly condition and repair (reasonable wear and tear, and damage by fire or other casualty excepted) and shall deliver and surrender the Leased Premises to the Landlord peaceably, together with all Tenant Improvements. The Landlord reserves the right, however, to require the Tenant at its cost and expense to remove any Alterations installed by the Tenant, and restore the Leased Premises to its original state, normal wear and tear excepted, unless Landlord has previously consented to allow such Alterations to remain. Prior to the expiration of the Lease term the Tenant shall remove all of its tangible property, fixtures and equipment from the Leased Premises. All property not removed by Tenant shall be deemed abandoned by Tenant, and Landlord reserves the right to charge the reasonable cost of such removal and disposal to the Tenant. If the Leased Premises are not surrendered at the end of the Lease term,

 

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the Tenant shall be liable for double rent under  NJSA  2A:42-6, and Tenant shall indemnify Landlord against Loss or liability resulting from delay by Tenant in surrendering the Leased Premises, including, without limitation any claims made by any succeeding tenant founded on the delay, and any loss of income suffered by Landlord. These covenants shall survive the termination of the Lease.

 

28. INDEMNITY

Anything in this Lease to the contrary notwithstanding, and without limiting the Tenant’s obligation to provide insurance hereunder, the Tenant covenants and agrees that it will indemnify, defend and save harmless the Landlord against and from all liabilities, obligations, damages, penalties, claims, costs, charges and expenses, including without limitation reasonable attorneys’ fees, which may be imposed upon or incurred by Landlord by reason of any of the following occurring during the term of this Lease:

(a) Any matter, cause or thing arising out of Tenant’s use, occupancy, control or management of the Leased Premises and any part thereof.

(b) Any negligence on the part of the Tenant or any of its agents, employees, licensees or invitees, arising in or about the Leased Premises.

(c) Any failure on the part of Tenant to perform or comply with any of its covenants, agreements, terms or conditions contained in this Lease.

Landlord shall promptly notify Tenant of any such claim asserted against it and shall promptly send to Tenant copies of all papers or legal process served upon it in connection with any action or proceeding brought against Landlord.

 

29. BIND AND CONSTRUE CLAUSE

The terms, covenants and conditions of this Lease shall be binding upon, and inure to the benefit of, each of the parties hereto and their respective heirs, successors and assigns. If any one of the provisions of this Lease shall be held to be invalid by a court of competent jurisdiction such adjudication shall not affect the validity or enforceability of the remaining portions of this Lease. The parties each acknowledge to the other that this Lease has been drafted by both parties, after consultation with their attorneys, and in the event of any dispute, the provisions are not to be interpreted against either party as the drafter of the Lease.

 

30. INCLUSIONS

The neuter gender when used herein, shall include all persons and corporations, and words used in the singular shall include words in the plural where the text of the instrument so requires.

 

31. DEFINITION OF TERM “LANDLORD”

When the term “Landlord” is used in this Lease it shall be construed to mean and include only the entity which is the owner of title to the building. Upon the transfer by the Landlord of the title, the Landlord shall advise the Tenant in writing by certified mail, return receipt requested, of the name of the Landlord’s transferee. In such event, the Landlord shall be automatically freed and relieved from and after the date of such transfer of title of all personal liability with respect to the performance of any of the covenants and obligations on the part of the Landlord herein contained to be performed, provided any such transfer and conveyance by the Landlord is expressly subject to the assumption by the transferee of the obligations of the Landlord hereunder.

 

32. COVENANTS OF FURTHER ASSURANCES

If, in connection with obtaining financing for the improvements on the Leased Premises, the mortgage lender shall request reasonable modifications in this Lease as a condition to such financing, Tenant will not unreasonably withhold, delay or refuse its consent thereto, provided that such modifications do not in Tenant’s reasonable judgment increase the obligations of Tenant hereunder or materially adversely affect the leasehold interest hereby created or Tenant’s use and enjoyment of the Leased Premises.

 

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33. COVENANT AGAINST LIENS

Tenant agrees that it shall not encumber, or permit to be encumbered, the Leased Premises or the fee thereof by any lien, charge or encumbrance, and Tenant shall have no authority to mortgage or hypothecate this Lease in any way whatsoever. Any violation of this Paragraph shall be considered a breach of this Lease.

 

34. SUBORDINATION

This Lease shall be subject and subordinate at all times to the lien of any mortgages or ground leases or other encumbrances now or hereafter placed on the land, Building and Leased Premises without the necessity of any further instrument or act on the part of Tenant to effectuate such subordination. However, Tenant agrees to execute such further documents solely evidencing the subordination of the Lease to the lien of any mortgage or ground lease as shall be desired by Landlord within 5 days, provided Landlord’s mortgagee agrees to a non-disturbance agreement.

 

35. EXCULPATION OF LANDLORD

Neither Landlord nor its principals shall have any personal obligation for the payment of any indebtedness or for the performance of any obligation under this Lease. The performance of Landlord’s obligations expressed herein may be enforced only against the Building and land of which the Leased Premises are a part, and the rents, issues and profits thereof. The Tenant agrees that no deficiency judgment or other judgment for money damages shall be entered by it against the Landlord or its principals personally in any action.

 

36. NET RENT

It is the intent of the Landlord and Tenant that this Lease shall yield, net to Landlord, the Base Rent specified and all Additional Rent and charges in each month during the term of the Lease, and that all costs, expenses and obligations of every kind relating to the Leased Premises shall be paid by the Tenant, unless expressly assumed by the Landlord.

 

37. SECURITY

Landlord currently holds a security deposit in the sum of $101,050.75 with regard to the Original Lease with Tenant for the Building. Landlord shall continue to hold that sum as the security deposit for this Lease and Tenant shall not be required to pay any additional security deposit.

 

38. BROKERAGE

The parties mutually represent to each other that Julian J. Studley, Inc. is the broker who negotiated and consummated the within transaction, and that neither party dealt with any other broker in connection with the Lease. In the event either party violates this representation, it shall indemnify and defend and hold the other party harmless from all claims and damages. It is agreed that the Landlord shall be responsible, at its sole cost and expense, to pay the brokerage commission in connection with this Lease.

 

39. LATE CHARGES

In addition to any other remedy, a late charge of 1-1/2% per month, retroactive to the date any Rent or payment for Tenant Improvements was due, shall be payable without notice from Landlord, on any such charges not paid within 5 days of the due date.

 

40. PRESS RELEASES

Subject to the prior written approval of Tenant (which shall not be unreasonably withheld), Landlord shall have the right to announce the execution of this Lease, the parties hereto, and the real estate brokers involved in such press releases as Landlord shall deem

 

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advisable. In addition, Tenant shall permit Landlord to use its name and photographs of the Leased Premises (all photographs being subject to Tenant’s prior consent) in Landlord’s marketing brochures and materials, and Tenant agrees to reasonably cooperate with Landlord in such regard, but at no cost or expense to Tenant.

 

41. WAIVER OF JURY TRIAL

Landlord and Tenant both irrevocably waive a trial by jury in any action or proceeding between them or their successors or assigns arising out of this Lease or any of its provisions, or Tenant’s use or occupancy of the Leased Premises.

 

42. LAWS OF NEW JERSEY

Without regard to principles of conflicts of laws, the validity, interpretation, performance and enforcement of this Lease shall be governed by and construed in accordance with the laws of the State of New Jersey. The sole and exclusive venue for any dispute between the parties shall be in Middlesex County, New Jersey.

 

43. OPTION TO RENEW

Provided the Tenant is not then in default hereunder, it has the right to renew the Lease, for two additional terms of 5 years each, to commence at the end of the prior term of this Lease. The renewal shall be upon the same terms and conditions as contained in this Lease, except that the Base Rent for the option term shall increase by 15% over the Base Rent for the year prior to the year in which the option term commences. The option of the Tenant to renew this Lease is expressly conditioned upon the Tenant delivering to the Landlord a notice, in writing, by certified mail, return receipt requested at least 180 days prior to the date fixed for termination of the then existing Lease term.

 

44. CROSS DEFAULT

Landlord and Tenant have entered into another lease at Eastpark at 8A for Suite 1002, in addition to this Lease. Any default, monetary or otherwise, in either lease shall give the Landlord the option to declare a default under both Leases. In the event of such a default, and exercise of this right by Landlord, it shall have all the rights set forth in either Lease.

IN WITNESS WHEREOF, the parties hereto have executed this document on the date first above written.

 

East Park at 8A

/s/    A. Joseph Stern, Partner

Pharmacopeia, Inc.

/s/    Joseph A. Mollica

 

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Exhibit 10.346

CERTAIN MATERIAL (INDICATED BY AN ASTERISK) HAS BEEN OMITTED FROM THIS DOCUMENT PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT. THE OMITTED MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION

LICENSE AGREEMENT

THIS LICENSE AGREEMENT (this “ Agreement ”) dated the 17 th day of December, 2008 (the “ Execution Date ”) is entered into by and between Ligand Pharmaceuticals Incorporated, a corporation organized and existing under the laws of the State of Delaware and having its principal office at 10275 Science Center Drive, San Diego, California 92121 (“ Ligand ”), and SmithKline Beecham Corporation, doing business as GlaxoSmithKline, a Pennsylvania corporation with its principal office at One Franklin Plaza, Philadelphia, Pennsylvania 19101 USA (“ GSK ”) (each, a “ Party ” and collectively, the “ Parties ”).

INTRODUCTION

WHEREAS , Ligand and GSK entered into that certain Research, Development and License Agreement dated as of December 29, 1994 under which GSK is developing and commercializing Promacta ® / Revolade ® (eltrombopag) (“ eltrombopag ”), (the “ Ligand/GSK Agreement ”);

WHEREAS , GSK and Ligand have been engaged in discussions relating to the development and ownership of the oral thrombopoietin mimetic which Ligand has designated as LGD-4665 (the “ Matter ”); and

WHEREAS , Ligand desires to exclusively license to GSK all of Ligand’s rights in and to LGD-4665, its back-ups, and all related compounds covered by patent rights of Ligand, as such Licensed Compounds are defined herein, in settlement of the Matter, and GSK is willing to take an exclusive license to all such Licensed Compounds, in each case pursuant to the terms and conditions as more particularly set forth in this Agreement.

NOW, THEREFORE , in consideration of the mutual covenants herein contained and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the Parties, intending to be legally bound, agree as follows:

ARTICLE 1

DEFINITIONS

When used in this Agreement, each of the following terms shall have the meanings set forth in this Article 1:

1.1 “ Affiliate ” means any corporation or other business entity controlled by, controlling or under common control with another entity, with “control” meaning direct or indirect beneficial ownership of more than fifty percent (50%) of the voting stock of, or more than a fifty percent (50%) interest in the income of, such corporation or other business entity, or such lower percentage as permitted under the relevant laws of the jurisdiction in which it is organized.

1.2 “ Business Day ” means a day other than a Saturday or Sunday on which banking institutions in New York are open for business.


CONFIDENTIAL

EXECUTION VERSION

 

1.3 “ Certificate of Analysis ” means certificates substantially in the form attached hereto in Exhibit A , evidencing the analytical tests conducted on a specific lot of Existing Licensed Compound and setting forth, inter alia , the items tested, specifications, and test results.

1.4 “ Combination Product ” means a Licensed Product that includes at least one other therapeutically effective active pharmaceutical ingredient (whether co-formulated or co-packaged with the Licensed Product, as the case may be, in such License Product) which is neither the Licensed Product nor part of the same molecule as that containing such Licensed Product. To be a Combination Product, the Combination Product and all its ingredients must be sold together as a single product and invoiced as one product. Drug delivery vehicles, adjuvants, and excipients shall not be deemed to be “therapeutically effective active pharmaceutical ingredients,” and their presence shall not be deemed to create a Combination Product.

1.5 “ Commercialization ” or “ Commercialize ” means any and all activities directed to and in support of the sale of a Licensed Product in the Field in the Territory, including, without limitation, marketing, promoting, market planning and product strategy, commercial-scale manufacturing, obtaining pricing and reimbursement approvals, negotiating with managed care and group purchasing organizations, professional and consumer promotion, advertising, distributing, offering for sale and selling, importing, conducting post-Regulatory Approval clinical studies, manufacturing for commercial sale (except for manufacturing scale-up activities, which shall be Development activities), medical affairs activities in support of a Licensed Product, including, without limitation, opinion leader development, medical inquiries, information and education and pharmacovigilance. When used as a verb, “Commercialize” means to engage in Commercialization.

1.6 “ Confidential Information ” means all all trade secrets, processes, formulae, data, information, improvements, inventions, chemical or biological materials, chemical structures, techniques, marketing plans, strategies, customer lists, or other information that has been created, discovered, or developed by a Party, or has otherwise become known to a Party, or to which rights have been assigned to a Party, as well as any other information and materials that are deemed confidential or proprietary to or by a Party (including, without limitation, all information and materials of a Party’s customers and any other Third Party and their consultants), in each case that are disclosed by such Party to the other Party, regardless whether any of the foregoing are marked “confidential” or “proprietary” or communicated to the other by the disclosing Party in oral, written, graphic, or electronic form. Any information or documents disclosed by a Party to the other Party that is subject to an ongoing confidentiality obligation at the Execution Date shall be deemed the disclosing Party’s Confidential Information under this Agreement and shall be subject to the provisions of Article 9.

1.7 “ Confidential Information of GSK ” has the meaning set forth in Section 9.1.1.

1.8 “ Control ” or “ Controlled ” means with respect to any (a) material, document, item of information, method, data or other know-how or (b) intellectual property right, the possession (whether by ownership or license, other than by a license granted pursuant to this Agreement) by a Party or its Affiliates of the ability to grant to the other Party access, ownership, a license and/or a sublicense as provided herein under such item or right without violating the terms of any agreement or other arrangement with any Third Party as of the time such Party would first be required hereunder to grant the other Party such access, ownership, license or sublicense.

 

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CONFIDENTIAL

EXECUTION VERSION

 

1.9 “ Covering ,” “ Cover ” or “ Covered ” means, with respect to a Patent Right, that, but for rights granted to a Party under such Patent Right, the practice by such Party of an invention claimed in such Patent Right would infringe a Valid Claim included in such Patent Right, or in the case of a Patent Right that is a patent application, would infringe a Valid Claim in such patent application if it were to issue as a patent.

1.10 “ Development ” or “ Develop ” means preclinical and clinical drug development activities, including, among other things: test method development and stability testing, toxicology, formulation, process development, manufacturing scale-up, development-stage manufacturing, quality assurance/quality control procedure development and performance with respect to clinical materials, statistical analysis and report writing, clinical studies, regulatory affairs, product approval and product registration (including pricing approvals).

1.11 “ Effective Date ” means the Execution Date.

1.12 “ Eltrombopag ” has the meaning set forth in the introduction to this Agreement.

1.13 “ Existing Licensed Compound ” means Ligand’s existing supply of LGD-4665 in bulk or finished form.

1.14 “ FDA ” means the United States Food and Drug Administration, or any successor agency.

1.15 “ FDCA ” means the federal Food, Drug, and Cosmetic Act, as amended, which is contained in Title 21 of the U.S. Code, section 301 et seq ., as amended and the regulations promulgated thereunder from time to time.

1.16 “ First Commercial Sale ” means, with respect to a particular country, the first bona fide invoiced sale of a Licensed Product to a Third Party by GSK or its Affiliates or sublicensees in such country after Regulatory Approval has been achieved for such Licensed Product in such country. Sales of Licensed Product for test marketing, sampling and promotional uses, clinical trial purposes or compassionate or similar use shall not be considered to constitute a First Commercial Sale.

1.17 “ Generic Product ” means any pharmaceutical product sold by a Third Party, not authorized by GSK or its Affiliate or sublicense, and approved in reliance on the prior approval of a Licensed Product as determined by the applicable regulatory authority, on the basis of it being comparable to and substitutable for such Licensed Product, as stated in a Regulatory Filing with such regulatory authority.

1.18 “ Know-How ” means inventions, discoveries, trade secrets, information, experience, data, formulas, procedures and results, including physical, chemical, biological, toxicological, pharmacological, clinical, and veterinary data, dosage regimens, control assays and product specifications, but excluding any Patent Rights.

 

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CONFIDENTIAL

EXECUTION VERSION

 

1.19 “ Laws ” means all laws, statutes, rules, regulations, ordinances and other pronouncements having the effect of law of any federal, national, multinational, state, provincial, county, city or other political subdivision, domestic or foreign.

1.20 “ Licensed Assets ” means the Licensed Compounds, Licensed Products, Licensed Patents and Licensed Know-How.

1.21 “ Licensed Compound ” means any and all thrombopoietin mimetics Controlled by Ligand or its Affiliate during the Term of the Agreement including: (a) that certain compound known as LGD-4665 with the molecular structure shown on Exhibit B attached hereto, and all formulations including intravenous formulations), salts, prodrugs, hydrates, solvates, polymorphs, enantiomers and isomers thereof; (b) any back-up compounds to LGD-4665 being developed by Ligand as of the Execution Date, as shown on, or incorporated by reference in, Exhibit B ; and (c) any other thrombopoietin mimetic compounds that are Covered by the Licensed Patents. Notwithstanding the foregoing, for the purpose of this Section 1.22, an “Affiliate” shall not include any Third Party which acquires control over Ligand or over which Ligand acquires control after the Execution Date so long as such Third Party does not otherwise become involved in the conduct of Development or Commercialization of the Licensed Compounds.

1.22 “ Licensed Product ” means any pharmaceutical preparation in any formulation or form containing one or more Licensed Compounds as its active ingredients for use in any field. Licensed Products shall include Combination Products.

1.23 “ Licensed Know-How ” means all Know-How that (a) is possessed as of the Execution Date by Ligand or its Affiliates, (b) is owned or Controlled by Ligand or its Affiliates as of the Execution Date, and (c) is necessary or useful in the use, development, design, registration, or sale of Licensed Compounds or Licensed Products. “ Licensed Know-How ” shall also include all Know-How discovered or developed by Ligand in connection with undertaking and completing the Ongoing Animal Studies and the Phase II Study referred to in Section 2.3. For the purpose of this Section, “Affiliate” shall exclude any Third Party that acquires control of Ligand or over which Ligand acquires control after the Execution Date so long as such Third Party does not otherwise become involved in the conduct of Development or Commercialization of the Licensed Products.

1.24 “ Ligand Liabilities ” has the meaning set forth in Section 2.5.

1.25 “ Licensed Patents ” means: (a) the Patent Rights identified on Exhibit C attached hereto, and (b) any and all Patent Rights that issue there upon in any jurisdiction in the world.

1.26 “ Major Market ” means any one of the following: Japan, United Kingdom, France, Germany, Italy, Spain or the United States.

1.27 “ Matter ” has the meaning set forth in the introduction to this Agreement.

1.28 “ NDA ” means (a) (i) a New Drug Application or Supplemental New Drug Application, as defined in Title 21 of the U.S. Code of Federal Regulations, Section 314.50, et.seq., which is submitted to the FDA, or any successor application or procedure, and (ii) any foreign counterpart of a U.S. New Drug Application, and (b) all supplements and amendments, including supplemental New Drug Applications (and any foreign counterparts), that may be filed with respect to the foregoing.

 

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CONFIDENTIAL

EXECUTION VERSION

 

1.29 “ Net Sales ” means the gross amount invoiced by GSK, its Affiliates or its sublicensees to independent Third Parties, whether end-users or distributors or agents (but who are not sublicensees), for the sale or transfer for value of a Licensed Product, less the following deductions to the extent actually incurred or allowed based upon the sale of such Licensed Product:

(a) credits, allowances, discounts and rebates to, and chargebacks from the account of, such Third Party for spoiled, damaged, out-dated and returned Licensed Product;

(b) freight and insurance costs for transporting such Licensed Product, to the extent invoiced to the Third Party;

(c) sales, value-added and other direct taxes on the sale of the Licensed Product;

(d) customs duties, surcharges and other governmental charges incurred in connection with the exportation or importation of such Licensed Product;

(e) trade, cash, and quantity discounts off the invoiced price and similar promotional discounts or rebates (such as management fees required by hospital buying groups or granted to managed care organizations) off the invoiced price;

(f) amounts reflecting retroactive price adjustments on sale of products, to the extent not previously deducted from net sales; and

(g) allowances or reserves for bad debt (including cost of collection); all of the foregoing to the extent consistent with United States generally accepted accounting principles applied on a consistent basis and in accordance with the normal practice in the industry.

For the avoidance of doubt, no Net Sales shall be calculated on Licensed Product delivered solely for research purposes, for clinical trials or distributed as free samples or promotions.

If GSK sells a Licensed Product with other products not covered by this Agreement, and GSK provides a discount, allowance or rebate to the purchaser of such products based on the invoiced prices for all products sold, such discount must be allocated pro rata based on average wholesale prices (“AWP”) across all such products and may not be applied disproportionately to the Licensed Product.

If GSK or its Affiliates or sublicensees receive non-cash consideration for Licensed Product sold or otherwise transferred to an independent Third Party, Net Sales will be determined based on the average of the gross invoice prices charged to other independent Third Parties in respect of cash sales during the applicable reporting period.

 

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CONFIDENTIAL

EXECUTION VERSION

 

1.30 “ Ongoing Animal Study(ies) ” means the [***] study and the [***] study on LGD-4665 conducted by Ligand.

1.31 “ Party ” means GSK or Ligand; “ Parties ” mean GSK and Ligand.

1.32 “ Patent Rights ” means all existing patents and patent applications and all patent applications hereafter filed and patents hereafter issued, including without limitation any continuations, continuations-in-part, divisions, provisionals or any substitute applications, any patent issued with respect to any such patent applications, any reissue, reexamination, renewal or extension (including any supplemental protection certificate) of any such patent, and any confirmation patent or registration patent or patent of addition based on any such patent, and all foreign counterparts of any of the foregoing.

1.33 “ Phase II Study ” means, as to a specific pharmaceutical product, a well conducted and lawful study, conducted anywhere in the world in diseased humans, of the feasibility, safety, dose ranging and efficacy of such product, that is prospectively designed to generate sufficient data (if successful) to commence a Phase III Trial (or foreign equivalent) of such product, as further defined in 21 C.F.R. 312.21(b), as amended from time to time, or the corresponding regulation in jurisdictions other than the United States. For the avoidance of doubt, a Phase II Trial requires enrollment of patients with the applicable disease or condition and is aimed to provide a measure of efficacy in addition to short-term tolerability. A Phase II Trial shall be deemed commenced upon the first dosing of the first patient.

1.34 “ Phase III Study ” means, as to a specific pharmaceutical product, a well conducted and lawful study in humans performed to gain evidence of the efficacy of such product in a target population, and to obtain expanded evidence of safety for such product that is needed to evaluate the overall benefit-risk relationship of such product and provide an adequate basis for physician labeling, as described in 21 C.F.R. 312.21(c), as amended from time to time, or the corresponding regulation in jurisdictions other than the United States. A Phase III Trial shall be deemed commenced upon the first dosing of the first patient.

1.35 “ Regulatory Approval ” means any and all approvals (excluding any applicable governmental price and reimbursement approvals), licenses, registrations or authorizations of any federal, national, multinational, state, provincial or local regulatory agency, department, bureau or other governmental entity that are necessary for the manufacture, use, storage, import, transport, promotion, marketing and sale of a product in a country or group of countries.

1.36 “ Regulatory Filings ” means, collectively, INDs, NDAs, drug master files and applications for designation of a product as an “Orphan Product(s)” under the Orphan Drug Act, or any other similar filings (including any foreign equivalents) for the clinical testing, manufacture or sale of a product.

1.37 “ Royalty Term ” has the meaning set forth in Section 7.3.1(b).

*** Certain information on this page has been omitted and filed separately with the Securities and Exchanged

Commission. Confidential treatment has been requested with respect to the omitted portions.

 

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CONFIDENTIAL

EXECUTION VERSION

 

1.38 “ Specifications ” means the handling, composition, testing, production, packaging, storage and shipping procedures and specifications for the Existing Licensed Compound.

1.39 “ Territory ” means all the countries of the world.

1.40 “ Third Party ” means any person or entity other than a Party or any of its Affiliates.

1.41 “ Valid Claim ” means a claim (a) of any issued, unexpired patent that has not been revoked or held unenforceable or invalid by a decision of a court or governmental agency of competent jurisdiction from which no appeal can be taken, or with respect to which an appeal is not taken within the time allowed for appeal, and that has not been disclaimed, denied or admitted to be invalid or unenforceable through reissue, disclaimer or otherwise or (b) of any patent application that shall not have been cancelled, withdrawn, abandoned or been pending for more than five (5) years from its earliest priority date claimed.

1.42 Construction . Any reference in this Agreement to an Article, Section, subsection, paragraph, clause, Schedule or Exhibit shall be deemed to be a reference to an Article, Section, subsection, paragraph, clause, Schedule or Exhibit, of or to, as the case may be, this Agreement, unless otherwise indicated. Unless the context of this Agreement otherwise requires, (a) words of any gender include each other gender, (b) words such as “herein”, “hereof”, and “hereunder” refer to this Agreement as a whole and not merely to the particular provision in which such words appear, (c) words using the singular shall include the plural, and vice versa, and (d) the words “include,” “includes” and “including” shall be deemed to be followed by the phrase “but not limited to”, “without limitation”, “inter alia” or words of similar import.

ARTICLE 2

DEVELOPMENT AND COMMERCIALIZATION ACTIVITIES

2.1 Overview . GSK shall have sole right, exercisable in GSK’s sole discretion and without accounting to Ligand, to control, direct and undertake all aspects of Developing and Commercializing Licensed Compounds and Licensed Products worldwide, including with regard to seeking, obtaining and maintaining Regulatory Approvals for the Licensed Compounds and Licensed Products in any jurisdiction in any field as well as manufacturing and having manufactured the Licensed Compounds and Licensed Products, including in each case making all strategic and tactical decisions with respect thereto. GSK covenants that it shall not knowingly violate any laws, rules and regulations that apply to the Development and Commercialization of the Licensed Compounds and Licensed Products. Ligand acknowledges and agrees that this Agreement is being entered into, in part, in order to settle the Matter and is not intended by the Parties to place on GSK the burden and expense of GSK having to Develop or Commercialize the Licensed Compounds or Licensed Products, unless, in its discretion, it chooses to do so. Further to the foregoing, for the avoidance of doubt, notwithstanding anything else in this Agreement, Ligand acknowledges and agrees that GSK shall be under no obligation, duty or diligence requirement to Develop or Commercialize the Licensed Compounds or Licensed Products, and that all decisions as to whether, if, when and how to undertake such Development or Commercialization activities shall be made by GSK in its sole discretion without taking into account any interest of Ligand and without having to consult with, advise or obtain any consent from Ligand.

 

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CONFIDENTIAL

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2.2 Ongoing Animal Studies . Prior to the Effective Date, Ligand had been undertaking the Ongoing Animal Studies involving LGD-4665. As soon as practical following the Effective Date, Ligand shall, at sole Ligand’s cost and expense, either complete or terminate the Ongoing Animal Studies. Ligand shall provide to GSK all data and study results, information and materials relating to or resulting from such activities of Ligand under or in connection with the Ongoing Animal Studies promptly after such data, results, information and materials come into the possession of Ligand and in substantially the same form as which they are received by Ligand.

2.3 Ligand’s Phase II Study for LGD-4665 . Prior to the Effective Date, Ligand had been undertaking one (1) active Phase II Study involving LGD-4665, Protocol No. LGD-4665-03. After the Execution Date of the Agreement, Ligand will use its commercially reasonable judgment to complete such study at Ligand’s sole cost in accordance with the study protocol as it exists as of the Execution Date. After the Execution Date, without the prior written consent of GSK (such consent not to be unreasonably withheld), Ligand will not alter the study protocol, will complete no more than the initial, planned enrollment of patients, and will not extend the Phase II Study. Ligand will keep GSK informed of the progress of the Phase II Study and will provide GSK with all data from such Phase II Study, including the final study report and SAS datasets, in substantially the same form as which it is received and maintained by Ligand. In addition, upon completion of the study, Ligand will promptly transfer the IND to GSK.

2.4 GSK Reports . GSK shall provide Ligand with brief, semi-annual reports summarizing its Development of Licensed Compounds. No reports shall be required after GSK makes and reports the First Commercial Sale of a Licensed Product in a Major Market. GSK shall promptly notify Ligand as soon as practicable after the occurrence of each milestone event set forth in Section 7.2. For the avoidance of doubt, GSK shall not wait until the next semi-annual report is due to inform Ligand of such milestone events, but instead shall do so promptly after the occurrence of the milestone event.

2.5 Ligand Liabilities In General . GSK shall not be the successor to Ligand, and GSK expressly does not assume and, without limitation to Section 13.1, shall not become liable to pay, perform or discharge, any liability, obligation or commitment whatsoever of Ligand. All liabilities, obligations or commitments of Ligand are referred to herein as the “ Ligand Liabilities ”. Ligand shall pay, perform and discharge when due, all of the Ligand Liabilities. Without limitation of the foregoing, the term “ Ligand Liabilities ” includes the following liabilities and obligations, whether accrued or fixed, absolute or contingent, known or unknown, determined or determinable, or otherwise (and whether due or to become due) and, unless otherwise expressly provided herein, whenever arising, and solely in the case of each of clause (i), (ii), (iii) and (iv) below, excluding any and all Liabilities GSK is obligated to indemnify, defend and hold harmless a Ligand Indemnified Party pursuant to Section 13.1:

(i) any liabilities, obligations or commitments of Ligand relating to or arising out of the assets other than the Licensed Assets;

(ii) any liabilities, obligations or commitments of any nature whatsoever of Ligand which arose or were incurred prior to the Execution Date, or which arise from or are based on events occurring or conditions existing before the Execution Date, including such liabilities, obligations or commitments of Ligand arising from or attributable to the ownership or use before the Execution Date of the Licensed Assets including, without limitation, any liability owing to Rockefeller University;

 

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(iii) and liabilities, obligations or commitments of any nature whatsoever of Ligand arising from Ligand’s Phase II Study for LGD-4665 referred to in Section 2.3; and

(iv) any liabilities, obligations or commitments under any contract with any Third Party.

ARTICLE 3

EXISTING LICENSED COMPOUND

3.1 Purchase of Existing Licensed Compound . At GSK’s sole discretion, GSK may elect, within [***] ([***]) months after the Effective Date, to purchase from Ligand (a) such amount in grams of bulk Existing Licensed Compound at a purchase price of [***] Dollars per kilogram ($[***]/kg) of bulk Existing Licensed Compound, and (b) such number of capsules of finished Existing Licensed Compound at a purchase price of [***] for each [***] capsules ($[***] capsules) of finished Existing Licensed Compound, in each case, on such other terms and conditions to be mutually agreed upon by the Parties. Exhibit D attached hereto details the amount of all bulk and finished Existing Licensed Compound existing as of the Execution Date for such quantities of Existing Licensed Compound. If GSK does not elect to purchase any Existing Licensed Compound from Ligand within [***] ([***]) months after the Effective Date, Ligand shall have the right to dispose of the Existing Licensed Compound or offer it for sale to a Third Party; provided, however , that prior to selling any Existing Licensed Compound to a Third Party, Ligand shall contact GSK to determine if it is interested in purchasing the Existing Licensed Compound on the same terms offered to the Third Party.

ARTICLE 4

REGULATORY MATTERS

4.1 Ownership . GSK shall own all Regulatory Approvals for Licensed Compounds and Licensed Products worldwide. Exhibit E sets forth the list of all Regulatory Filings worldwide that relate to the Licensed Compounds and/or Licensed Products and which exist as of the Execution Date. The Parties shall take all appropriate actions and make all necessary filings (at Ligand’s cost and expense) to transfer to GSK all right, title and interest in and to such Regulatory Filings.

4.2 Regulatory Coordination, Filings, Meetings and Correspondence . GSK shall oversee, monitor and coordinate all regulatory actions, communications and filings with and submissions to regulatory authorities, including filings and submissions of supplements and amendments thereto, with respect to each Licensed Compound or Licensed Product. GSK shall have the sole responsibility for drafting all Regulatory Filings for Licensed Products and shall be solely responsible for interfacing, corresponding and meeting with regulatory authorities with respect to all Licensed Compounds and Licensed Products. GSK shall have the exclusive right to file for,

 

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request and maintain any regulatory exclusivity rights for Licensed Products (including regulatory exclusivity rights based upon an orphan drug designation of a Licensed Product) and to conduct and prosecute any proceedings or actions to enforce such regulatory exclusivity rights.

4.3 Assistance . Ligand shall cooperate with GSK to provide all reasonable assistance and take all actions reasonably requested by GSK that are necessary or useful to enable GSK to comply with its obligations, and exercise its rights, under this Agreement.

ARTICLE 5

TRANSFER OF INFORMATION, LICENSED KNOW-HOW

5.1 Existing Information and Licensed Know-How . Within [***] ([***]) days following the Effective Date, Ligand shall, without any consideration in addition to that which is expressly required pursuant to this Agreement and without any royalty obligation, transfer and cause to be transferred to GSK complete copies of the information from the electronic data room established by Ligand to which GSK had access prior to the Execution Date. This information shall include, without limitation, the following: (a) all preclinical and clinical data and study results, Regulatory Filings, Regulatory Approvals, material regulatory correspondence, studies, information, safety and efficacy information relating to any Licensed Compounds and/or any Licensed Products and/or the Development thereof by or behalf of Ligand prior to the Effective Date, and (b) all information known to Ligand regarding the handling, precautions, toxicity and hazards associated with the Existing Licensed Compound, all as more specifically set forth in Exhibit F , attached hereto and incorporated herein.

ARTICLE 6

LICENSES; COVENANTS; RELEASE

6.1 Grant . Subject to the terms and conditions of this Agreement, Ligand hereby grants to GSK an exclusive (even as to Ligand) royalty-bearing, worldwide, perpetual, irrevocable right and license under the Licensed Patents and Licensed Know-How in the Territory to Develop, Commercialize, make, have made, use, have used, import, sell, offer for sale and have sold Licensed Compounds and Licensed Products in any and all fields in the Territory. Such license shall further include the right to grant sublicenses to Affiliates of GSK and to Third Parties in accordance with the terms set forth in Section 6.2. For the avoidance of doubt, Ligand shall retain rights under the Licensed Patents and Licensed Know-How to use LGD-4665 and other Licensed Compounds for its internal or partnered research and development purposes, subject to Section 6.4 and Section 6.5. For example, Ligand shall have the right to conduct cross-reactivity testing using thrombopoietin related assays in the research and development of non- thrombopoietin related compounds (e.g., compounds that impact the EPO, interferon or GCSF related signaling pathways).

6.2 Sublicense Rights . The licenses granted pursuant to Section 6.1 shall be fully sublicensable. GSK shall give Ligand written notice of any such sublicense in a Major Market, including the identity of the sublicense. GSK shall be jointly and severally responsible with its sublicensees to Ligand for failure by its sublicensees to comply with, and GSK guarantees the compliance by each of its sublicensees with, all such applicable restrictions and limitations in accordance with the terms and conditions of this Agreement.

 

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6.3 No Implied Licenses Or Rights . Except as expressly provided in this Agreement, neither Party shall have any license or other interest in any intellectual property rights Controlled by the other Party.

6.4 Non-Compete . As a condition of this Agreement, Ligand covenants to GSK, effective as of the Execution Date, during the Royalty Term and for [***] ([***]) [***] thereafter, that Ligand and its Affiliates shall not, directly or indirectly, Develop, Commercialize, make, have made, use, have used, import, sell, offer for sale or have sold any thrombopoietin mimetic products. For the avoidance of doubt, notwithstanding the previous sentence, Ligand shall be able to directly or indirectly, Develop, Commercialize, make, have made, use, have used, import, sell, offer for sale or have sold any products that do not demonstrate, as their predominant or primary property, agonist activity at the thrombopoietin receptor. Notwithstanding the foregoing, for the purpose of this Section 6.4, an “Affiliate” shall not include any Third Party which acquires control over Ligand after the Execution Date or any Third Party to which Ligand assigns this Agreement in accordance with Section 13.3. For the avoidance of doubt, nothing herein shall prevent Ligand from acquiring control over a Third Party, provided that Ligand complies with the first sentence of the Section 6.4.

6.5 Further Covenant of Ligand .

(a) Ligand covenants to GSK, effective as of the Effective Date, that during the Royalty Term, Ligand and its Affiliates (which, for the purpose of the entirety of the Section 6.5(a), excludes any Third Party which acquires control over Ligand after the Execution Date or any Third Party to which Ligand assigns this Agreement in accordance with Section 13.3) will not file in any jurisdiction any patent application that Covers any Licensed Compound, Licensed Product and/or eltrombopag, unless Ligand or its Affiliates are requested to do so by GSK. In the event that Ligand or any of its Affiliates, in violation of the foregoing covenant, inadvertently files or otherwise obtains Patent Rights that Covers Licensed Compound, Licensed Product and/or eltrombopag (any such Patent Rights to the extent it Covers Licensed Compound, Licensed Product and/or eltrombopag, a “ New Product Patent ”), Ligand hereby covenants to GSK and its Affiliates and sublicensees, effective as of the Execution Date, that none of Ligand or any of its Affiliates will: (i) sue GSK, its Affiliates or sublicensees for infringement of, or (ii) commence, aid, prosecute, or cause to be commenced, aided or prosecuted any action or other proceeding against GSK, its Affiliates or sublicensees with respect to infringement of, in each case ((i) and (ii)), any New Product Patent. For the avoidance of doubt, this section shall not restrict the right of any Third Party which acquires control over Ligand or a successor or assign of Ligand to (i) sue GSK, its Affiliates or sublicensees for infringement of, or (ii) commence, aid, prosecute, or cause to be commenced, aided or prosecuted any action or other proceeding against GSK, its Affiliates or sublicensees with respect to infringement of, in each case ((i) and (ii)), any patent other than the Licensed Patents listed on Exhibit C .

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(b) Ligand further covenants to GSK, effective as of the Effective Date, that during the Royalty Term, with respect to (i) any Third Party which acquires control over Ligand after the Execution Date, (ii) any Third Party to which Ligand assigns this Agreement in accordance with Section 13.3, or (iii) any Third Party which Ligand acquires after the Execution Date (together, the “Section 6.5(b) Affiliates”), none of such Section 6.5(b) Affiliates of Ligand or any of their respective sublicensees will: (x) sue GSK, its Affiliates or sublicensees for infringement of, or (y) commence, directly aid, prosecute, or cause to be commenced, directly aided or prosecuted any action or other proceeding against GSK, its Affiliates or sublicensees with respect to infringement of, in each case ((x) and (y)), any patent or patent application owned or Controlled by such Section 6.5 Affiliate or sublicensee that is necessary for GSK, its Affiliates or sublicensees to practice the inventions in the Licensed Patents, including, without limitation, the Licensed Compounds and any Licensed Product.

6.6 Section 365(n) of The Bankruptcy Code . All rights and licenses granted under or pursuant to any section of this Agreement are, and shall otherwise be deemed to be, for purposes of Section 365(n) of the Bankruptcy Code, licenses of rights to “intellectual property” as defined under Section 101(35A) of the Bankruptcy Code. The Parties shall retain and may fully exercise all of their respective rights and elections under the Bankruptcy Code. Upon the bankruptcy of any Party, the non-bankrupt Party shall further be entitled to a complete duplicate of (or complete access to, as appropriate) any such intellectual property, and such, if not already in its possession, shall be promptly delivered to the non-bankrupt Party, unless the bankrupt Party elects to continue, and continues, to perform all of its obligations under this Agreement.

6.7 Settlement and Release . As of the Effective Date, (a) GSK, on behalf of itself and its Affiliates, hereby releases and discharges Ligand and its respective subsidiaries, divisions, parents, Affiliates, agents and each of their respective officers, directors, employees, representatives and agents, and (b) Ligand, on behalf of itself and its Affiliates, hereby releases and discharges GSK and its subsidiaries, divisions, parents, Affiliates, agents and each of their respective officers, directors, employees, representatives and agents, in each case ((a) and (b)), as follows:

(i) from any and all actions, claims, counterclaims, defenses and damages whatsoever, in law or equity, whether in tort or contract or otherwise, which the releasing Party ever had, now has or hereafter shall or may have, that can be, could be or could have been asserted by GSK or Ligand in the Matter, or any other judicial or non-judicial proceeding based on facts and circumstances as of the Effective Date known or unknown to the releasing Party which arise out of or relate to any allegations, facts or occurrences alleged in the Matter;

(ii) from any and all actions, claims, counterclaims, defenses and damages whatsoever, in law or equity, whether in tort or contract or otherwise, which the releasing Party has or may have had as of the Effective Date, that can be, could be or could have been asserted by GSK or Ligand relating to the Ligand/GSK Agreement, or any other judicial or non-judicial proceeding based on facts and circumstances as of the Effective Date known to the releasing Party which arise out of or relate to the Ligand/GSK Agreement; and

 

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(iii) from any and all actions, claims, counterclaims, defenses and damages whatsoever, in law or equity, whether in tort or contract or otherwise, which the releasing Party has or may have had as of the Effective Date, that can be, could be or could have been asserted by GSK or Ligand relating to Ligand’s EPO, G-CSF, and interferon research programs with respect to compounds in such programs identified by Ligand after 2002 or any other judicial or non-judicial proceeding based on facts and circumstances as of the Effective Date known or unknown to the releasing Party which arise out of or relate to Ligand’s EPO, G-CSF, and interferon research programs, but only with respect to compounds in such programs identified by Ligand after 2002;

provided, however , with respect to (i), (ii) and (iii) above, that nothing herein shall have any effect on any actions, claims, counterclaims, defenses or damages related to any alleged breach of this Agreement, including any alleged breach of any representations, warranties and covenants therein; and provided, further, however, that nothing in (ii) or (iii) above shall have any effect on any patent claims GSK may have, now or in the future, relating to Ligand’s EPO, G-CSF and interferon programs. For the avoidance of doubt, this settlement and release shall not apply to any future conduct that has not occurred as of the Effective Date and shall in no way prevent the Parties from bringing any actions, claims, counterclaims, defenses and damages whatsoever, in law or equity, whether in tort or contract or otherwise in the future based on conduct that first occurs after the Effective Date. Furthermore, and for the avoidance of doubt, nothing herein shall have any effect on any indemnification obligations of a Party for Third Party claims as set forth in Article 13.

6.8 No Admissions . Nothing contained in this Agreement, and none of the execution, delivery, or performance of any obligation of or under this Agreement, shall be construed as an admission by any Party of any wrongdoing, liability or potential claims, and the Parties recognize that each expressly denies any liability or potential liability.

6.9 No Effect on Ligand/GSK Agreement . Nothing in this Agreement shall have any impact on GSK’s payment obligations or GSK’s or Ligand’s other obligations under the Ligand/GSK Agreement as they relate to eltrombopag. For the avoidance of doubt, GSK expressly confirms that it has an obligation to pay Ligand royalties on sales of eltrombopag, as set forth in the Ligand/GSK Agreement.

ARTICLE 7

FINANCIAL PROVISIONS

7.1 License Fee . Within five (5) Business Days after the Execution Date and receipt of an invoice from Ligand, GSK shall pay a license fee of Five Million Dollars ($5,000,000) in cash to Ligand by wire transfer of immediately available funds into an account designated by Ligand. Such license fee shall be nonrefundable and noncreditable against any other payments due hereunder.

7.2 Milestone Payments .

 

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7.2.1 Licensed Compounds/Licensed Products . Subject to Section 7.6, GSK shall pay Ligand, in the manner set forth in Section 7.4, the following non-refundable and non-creditable amounts no later than [***] ([***]) days after the occurrence of the corresponding milestone events and receipt by GSK of an invoice from Ligand requesting payment of such milestone. Each payment under this Section 7.2.1 shall be made only once during the Term and only if and upon each particular milestone event being satisfied pursuant to its term set forth in the following table.

 

Milestone

   Payment

[***]

   $[***]

[***]

   $[***]

[***]

   $[***]

[***]

   $[***]

7.2.2 Sales Milestone . Subject to Section 7.6, GSK shall pay Ligand, in the manner set forth in Section 7.4, a [***] Dollars ($[***]) no later than[***] ([***]) days after the end of the first calendar quarter in which [***].

7.2.3 Notices; Further Clarification . GSK shall promptly notify Ligand of the occurrence of each milestone. If any milestone set forth above is achieved prior to or in the absence of the achievement of any preceding milestone for such Licensed Compound or Licensed Product then, effective upon achievement of any such milestone, all previously unpaid payments for any such preceding milestone shall also become due and payable.

7.3 Royalties .

7.3.1 Licensed Products .

(a) During the Royalty Term, GSK shall pay to Ligand royalties on annual aggregate Net Sales of each Licensed Product in the Territory, on a country-by-country basis, as follows:

(i) For the first twelve (12) months beginning with the First Commercial Sale in a country, at a royalty rate of eight percent (8%) of Net Sales; and

(ii) Thereafter, at a royalty rate of sixteen percent (16%) of Net Sales.

For clarity, a partial initial month in which the First Commercial Sale occurs shall be considered a full month for purposes of subsection (i) above.

(b) Royalties shall be payable, on a country-by-country basis, on Net Sales of Licensed Products for the longer of: (i) the expiration of the last-to-expire of the Licensed Patents with a Valid Claim Covering the composition of matter or therapeutic use for a labeled indication of the Licensed Product in such country (including any additional data exclusivity, as may be available under applicable Law), or (ii) ten (10) years from the date of First Commercial Sale of the first Licensed Product in any country worldwide (“Royalty Term”). The Royalty Term shall begin on the Effective Date and continue until the date the last royalty payment obligation expires in the last country for any Licensed Product as set forth above in this Section 7.3.1(b).

 

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(c) The royalties set forth in this Section 7.3.1 shall be reduced in the following situations:

(i) In the absence of a Valid Claim within the Ligand Patent Rights Covering the composition of matter or use of a Licensed Product at the time of sale and in the country of sale of the Licensed Product, but where Ligand owns or Controls a pending patent application within the Ligand Patents, GSK shall pay to Ligand royalty payments at [***] percent ([***]%) of the relevant royalty rate that would otherwise be payable under this Section 7.3.1 for a period of [***] ([***]) years from the date of First Commercial Sale of the Licensed Product at issue (subject to subsection (ii) below), and shall pay the remaining [***] ([***]%) of the relevant royalty rate in escrow as provided below, until the earlier of (A) such time as a Valid Claim within the Ligand Patent Rights Covering the composition of matter or use of a Licensed Product issues with respect to such pending patent application in such country, in which case Section 7.3.1(a) shall apply; or (B) the date which is [***] ([***]) years from the date of First Commercial Sale of the Licensed Product at issue. The payments accruing under the remaining [***] percent ([***]%) of the relevant royalty rate shall be deposited into an escrow account to be maintained by GSK on behalf of Ligand (with interest from such account being reinvested into such account). Upon the occurrence of subsection (A) herein prior to [***] ([***]) years from the date of First Commercial Sale of the Licensed Product at issue, the remaining [***] percent ([***]%) of such payments (and interest) shall be promptly paid to Ligand. In the event a Valid Claim within the Ligand Patent Rights does not issue within such time frame, GSK shall retain all such amounts paid into escrow.

(ii) In the event a Licensed Product is sold in a county and a Generic Product is sold in such country during the Royalty Term, then at the end of the first [***][***]([***]) day period (the “ Generic Entry Period ”) during which one or more Third Parties sell a number of units of a relevant Generic Product in such country that comprises [***] percent ([***]%) or more of the aggregate number of units of such Licensed Product sold in such country during such Generic Entry Period (based upon mutually acceptable Third Party objective data sources), the otherwise applicable royalty rate set forth in this Section 7.3.1 shall be reduced by [***] percent ([***]%) after the conclusion of the Generic Entry Period.

(d) GSK shall have sole discretion, authority and right with respect to determining whether to enter into an agreement for license or other rights and to incur an obligation for any Third Party intellectual property required to make, have made, use, sell, lease, offer to sell or lease, import, export (within the Territory) or otherwise exploit, or transfer physical possession of or title in, an Licensed Product for any use in a country in the Territory. If any royalties or other payments are due to Third Parties, with respect to the identification, discovery, development, manufacture, use or sale of Licensed Compounds or Licensed Products

 

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(such payments, “ GSK Third Party Payments ”), then GSK shall be solely responsible for payment of all such royalties or other payments; provided howeve r, that GSK shall have the right to deduct [***] percent ([***]%) of such GSK Third Party Payments from the otherwise applicable royalties payable to Ligand for such particular calendar quarter; provided further , however, that in no event shall the otherwise applicable royalty rate to Ligand be reduced by more than [***] percent ([***]%) in a given calendar quarter. GSK shall have the right to carry forward and apply any such unused offset or deduction to which GSK is entitled in future calendar quarters or years in the event that such [***] percent ([***]%) reduction threshold would be exceeded, until the full amount of offset or deduction to which GSK is entitled is satisfied.

7.3.2 Cumulative Royalties . The obligation to pay royalties on the Net Sales of a Licensed Product shall be imposed only once with respect to the same unit of said Licensed Product regardless of the number of Valid Claims Covering such Licensed Product.

7.3.3 Compulsory Licenses . Should a compulsory license be granted to a Third Party under the applicable Laws of any country in the Territory under the Ligand Patents licensed hereunder to GSK, the royalty rate payable for sales of Licensed Products in such country shall be adjusted to match any lower royalty rate granted to such Third Party for such country, with respect to the sales of such Licensed Products, and during such periods for which such Third Parties sell under the compulsory license material quantities of products that compete with the Licensed Products then marketed and sold by GSK in that country.

7.3.4 Royalties for Combination Products . In the event that GSK develops a Combination Product, the following provisions will apply with respect to the calculation of royalties on the sale of such Combination Products. Net Sales of Combination Products shall be calculated separately from Net Sales of Licensed Products.

For purposes of calculating the amount of Net Sales with respect to Combination Products sold in each Royalty Period, the Parties agree to use the following formula:

    A    

(A + B)

Multiplied by the Total Net Sales of Combination Products for such Royalty Period

Where:

A equals the actual average of the invoice price of the most frequently prescribed dose of the Licensed Product containing the same compound that is part of the Combination Product in each of the Major Market countries, if such Licensed Product is sold separately (i.e. not as part of a Combination Product), and B equals the sum of the actual average of the invoice prices of the most frequently prescribed dose of all other therapeutically or prophylactically active ingredients in the Combination Product other than the Licensed Compound in each of the Major Market countries, if such other active ingredients are sold separately.

 

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For purposes of calculating Net Sales for Combination Products, if the Licensed Product or the other therapeutically or prophylactically active ingredients are not sold separately in all of the Major Market countries, then the Parties will calculate the averages referenced above, using the prices in those Major Market countries for which the Product and the other ingredients are sold separately. If, however, the Licensed Product or the other therapeutically or prophylactically active ingredients are not sold separately in any of the Major Market countries, then the Parties will negotiate in good faith an appropriate calculation of Net Sales that are subject to the royalty payment obligation under this Agreement so as to fairly allocate the relative value of the active ingredients in the Combination Product; provided, however , that the Parties agree that the multiplier applied to the royalty rate or Net Sales totals for such Combination Product will be less than 1 and not a negative number.

7.3.5 GSK License Paid-Up . Upon the expiration of the Royalty Term, the license granted under Section 6.1 shall become fully paid-up and royalty-free, but otherwise not be amended or effected, and shall remain in full force and effect.

7.4 Royalty Reports; Payments .

7.4.1 Reporting . Following the First Commercial Sale of the first Licensed Product in any country worldwide and continuing during the Royalty Term, GSK shall make payments and written reports to Ligand within [***] ([***]) days after the end of each calendar quarter with respect to the Net Sales of Licensed Products and royalties owed by GSK, its Affiliates or sublicensees hereunder, each such written report stating for the period in question: (i) for Licensed Product disposed of by sale, the quantity and description of Licensed Product, (ii) for Licensed Product disposed of other than by sale, the quantity, description, and nature of the disposition, (iii) the calculation of Net Sales for such quarter including the amount of such sales in foreign currencies on a country-by-country basis and the conversion under this Section 7.4, and (iv) the calculation of the amount due to Ligand for such quarter pursuant to Section 7.3 on account of such Net Sales. Such reports shall also detail if and when any applicable milestone event occurs under Section 7.2.2 and the payment due thereunder.

7.4.2 Payment . The information contained in each report under Section 7.4.1 shall be considered Confidential Information of GSK. Concurrent with the delivery of each quarterly report, GSK shall make the payment due Ligand hereunder for the calendar quarter covered by such report by wire transfer to a bank designated in writing by Ligand.

7.4.3 Conversion . Net Sales of Licensed Product made in currencies other than the U.S. Dollar shall be converted by GSK pursuant to its internal global sales reporting procedures.

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7.4.4 Late Payments . GSK shall pay interest to Ligand on the aggregate amount of any payments that are not paid on or before the date such payments are due under this Agreement at a rate per annum equal to the lesser of the prime rate of interest plus [***] percent ([***]%), as reported by THE WALL STREET JOURNAL, calculated on the number of days such payments are paid after the date such payments are due.

7.5 Accounting . GSK agrees to keep complete and accurate books and records pertaining to Net Sales of Licensed Products for a period of at least three (3) years after the relevant payment is owed pursuant to this Agreement, setting forth the sales and other disposition of Licensed Product sold or otherwise disposed of in sufficient detail to enable royalties and compensation payable to Ligand hereunder to be determined. GSK further agrees to permit such books and records to be examined by an independent accounting firm selected by the Ligand (and reasonably acceptable to GSK) to verify reports provided for in Section 7.4. Unless Ligand obtains the prior written consent of GSK, such accounting firms must be selected from among the four largest international accounting firms. Such audit shall not be performed more frequently than once per calendar year nor more frequently than once with respect to records covering any specific period of time. Such examination is to be made at the expense of Ligand, except in the event that the results of the audit reveal a discrepancy in favor of GSK of [***] percent ([***]%) or more over the period being audited, in which case reasonable audit fees for such examination shall be paid by GSK. If such accounting firm correctly concludes that additional royalties were owed during such period, GSK shall pay the additional royalties within thirty (30) days of the date Ligand delivers to GSK such accounting firm’s written report so correctly concluding. If such accounting firm correctly concludes that excess royalties were paid during such period, Ligand shall refund the excess royalties within thirty (30) days of the date Ligand receives such accounting firm’s written report so correctly concluding. Ligand shall treat all information subject to review under this Section 7.5 or under any sublicense agreement in accordance with the confidentiality provisions of Article 9 and shall cause such independent accounting firm to enter into an acceptable confidentiality agreement with GSK obligating such firm to retain all such financial information in confidence pursuant to such confidentiality agreement. Any such independent accounting firm acting under this Section 7.5 shall limits its disclosures to Ligand to be whether or not the correct payments have been made, and if the correct payments have not been made, then what the correct payments should have been and what the difference is from the actual payments that had been made.

7.6 Tax Matters . Any income or other taxes that a paying Party is required by law to pay or withhold on behalf of a receiving Party with respect to royalties or other payments payable to a receiving Party under this Agreement shall be deducted from the amount of such royalties or other payments due, and paid or withheld, as appropriate, by the paying Party on behalf of the receiving Party. Any such tax required by law to be paid or withheld shall be an expense of, and borne solely by, the receiving Party. The paying Party shall furnish the receiving Party with reasonable evidence of such payment or amount withheld, in electronic or written form, as soon as practicable after such payment is made or such amount is withheld. The Parties will reasonably cooperate in completing and filing documents required under the provisions of any applicable tax laws or under any other applicable law in connection with the making of any required tax payment or withholding payment, or in connection with any lawful claim to a refund of or credit for any such payment.

 

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Commission. Confidential treatment has been requested with respect to the omitted portions.

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ARTICLE 8

INTELLECTUAL PROPERTY OWNERSHIP, PROTECTION AND RELATED MATTERS

8.1 Ownership . Inventorship of patentable inventions conceived or reduced to practice during the course of the performance of activities pursuant to this Agreement shall be determined in accordance with the applicable U.S. patent laws. All right, title and interest of Ligand in and to any and all patentable inventions conceived or reduced to practice during the course of completing the Ongoing Animal Studies shall be and hereby is assigned to GSK. All right, title and interest of Ligand in and to any and all patentable inventions relating to the Licensed Compounds or Licensed Products conceived or reduced to practice whether solely by GSK, its Affiliates and sublicensees or whether by such parties jointly with Ligand or its Affiliates as joint inventors under applicable law, during the Royalty Term shall be and hereby is assigned to GSK.

8.2 Prosecution of Licensed Patents .

8.2.1 GSK shall have the first right, but not the obligation, to prosecute and maintain the Licensed Patents. GSK shall pay [***] of the filing costs and fees incurred with respect to the prosecution and maintenance of such Licensed Patents. If GSK exercises its right to prosecute and maintain the Licensed Patents, GSK shall have complete discretion over such prosecution and maintenance of Licensed Patents including, without limitation, deciding in which countries to prosecute and maintain any of the Licensed Patents and the manner in which to prosecute and maintain the respective Licensed Patents.

8.2.2 On the reasonable request of GSK, Ligand shall cooperate, in all reasonable ways, in connection with the prosecution of all patent applications included within such Licensed Patents including, without limitation, granting GSK a power of attorney to permit it to prosecute the Licensed Patents; provided, however, in Ligand’s reasonable opinion, such cooperation or prosecution activities do not risk having an adverse impact any other patents or patent applications owned or Controlled by Ligand.

8.3 Enforcement and Defense of Licensed Patents .

8.3.1 If either Party becomes aware of any Third Party activity that infringes a Licensed Patent, then that Party shall give prompt written notice to the other Party regarding such alleged infringement. As between the Parties, GSK shall have the first right, but not the obligation, to attempt to resolve such alleged infringement by commercially appropriate steps at its own expense, including, without limitation, the filing of an infringement suit using counsel of its own choice.

8.3.2 If GSK fails to resolve such alleged infringement or to initiate a suit with respect thereto within one hundred eighty (180) days after the notice provided under Section 8.3.1, then, Ligand shall have the right, but not the obligation, to attempt to resolve such infringement by commercially appropriate steps at its own expense, including without limitation the filing of an infringement suit using counsel of its own choice.

 

*** Certain information on this page has been omitted and filed separately with the Securities and Exchanged

Commission. Confidential treatment has been requested with respect to the omitted portions.

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8.3.3 Any amounts recovered as a result of an action pursuant to this Section 8.3, whether by settlement or judgment, shall be allocated first to reimburse each Party for any costs and expenses incurred by such Party (and not otherwise reimbursed). Any remaining recovery shall be shared by the Parties in proportion to the percentage of litigation expenses funded by each Party.

8.3.4 In any event, at the request and expense of the Party bringing an infringement action under this Section 8.3, the other Party agrees to be joined as a party to the suit if necessary for the initiating Party to bring or continue an infringement action hereunder and to provide reasonable assistance in any such action. Neither Party may settle any action or proceeding brought under this Section 8.3 in a manner that, or knowingly take any other action in the course thereof that, materially adversely affects the other Party’s interest in the Licensed Patents, without the written consent of such other Party, which consent, shall not be unreasonably withheld. Each Party shall always have the right to be represented by counsel of its own selection and its own expense in any suit or other action instituted by the other Party pursuant to this Section 8.3 for such infringement. The amounts borne by such Party pursuant to the preceding sentence shall not count towards the determination of the allocation between the Parties of any remaining recovery pursuant to Section 8.3.3.

8.4 Defense of Third Party Infringement Claims . If, after the Effective Date, a Third Party asserts that a Patent or other right Controlled by it is infringed by a Party’s activities relating to a Licensed Compound or Licensed Product or a Party becomes aware of Patent Rights or other right that might form the basis for such a claim, the Party first obtaining knowledge of such a claim or such potential claim shall promptly provide the other Party with notice thereof and the related facts in reasonable detail. GSK shall control and direct the defense of any such claim or potential claims as well as all settlement discussions, including obtaining license(s) from such Third Party(ies). Neither Party shall be required to conduct any work under this Agreement which it believes in good faith may infringe Third Party patent or other intellectual property rights. This Section 8.4 shall not be interpreted as placing on either Party a duty of inquiry regarding Third Party intellectual property rights. GSK shall be responsible for payment of any award of damages arising from or related to a Third Party infringement claim arising after the Effective Date, except to the extent such claim or damages are covered by a breach of a representation or warranty made by Ligand under this Agreement or are otherwise covered by Ligand’s indemnification of GSK under Section 13.1.2 in which case the provisions of Section 13.1 shall provide for the allocation and timing of payment responsibility for such damages.

8.5 Patent Term Extensions . GSK shall be solely responsible for making all decisions regarding patent term extensions, including supplementary protection certificates and any other extensions that are now or become available in the future, that are applicable to Licensed Patents. Ligand shall reasonably cooperate, as requested by Ligand, to implement such decisions.

 

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8.6 Cooperation . Each Party hereby agrees: (a) to use commercially reasonable efforts to work together with the other Party to file, prosecute and maintain Patent Rights under this Article 8 that include claims of appropriate scope to provide optimal patent protection for all Licensed Products; and (b) to provide the other Party with copies of all material correspondence with the U.S. Patent and Trademark Office or its foreign counterparts pertaining to prosecution and maintenance of Patent Rights hereunder and as to which such Party has a license under this Agreement reasonably in advance of any relevant filing deadline or intended filing date for such other Party to review and comment thereon, to incorporate, absent a substantial reason to the contrary, the non-filing Party’s comments on such filing before submitting such filing to the relevant patent authority, and to provide the other Party a copy of all material notices received from a patent authority with respect thereto.

8.7 Perfection of Interest . Each Party shall cooperate with the other and take all reasonable additional actions and execute such agreements, instruments and documents as may be reasonably required to perfect the other’s ownership interest in accordance with the intent of this Agreement including, without limitation, the execution of necessary and appropriate instruments of assignment to achieve such joint ownership as set forth in Section 8.2 and the provision, on a reasonable basis, of its employees, agents, consultants and independent contractors to the other Party (or to the other Party’s authorized attorneys, agents or representatives), to the extent reasonably necessary to enable the prosecuting Party to undertake Patent Prosecution for Program Inventions as provided herein.

8.8 Trademarks . GSK shall, at its sole expense, select, register, own and enforce all trademarks for Licensed Products.

8.9 Negative Pledge . Ligand represents, warrants, and covenants that there are no liens or claims currently existing on or to the Licensed Patents (including any liens or claims on or to rights to sue for past, present and future infringements thereof, any licenses, claims, damages, and proceeds of suit arising therefrom, or any payments or rights to payments arising out of the sale, lease, license, assignment, or other disposition thereof), any additions to, and substitutions for, any or all of the foregoing or any “proceeds” (as defined in Article 9 of the Uniform Commercial Code) of any or all of foregoing, including that could reasonably be expected to adversely affect GSK’s benefits and rights under this Agreement. Ligand shall not create, incur, or permit to exist on or to any Licensed Patents, shall defend such Licensed Patents against, and shall take such other action as is necessary to remove in respect to such Licensed Patents, any lien or claim, other than the liens or claims created hereby. Further, Ligand covenants and agrees not to enter into any agreements which would prohibit the creation or attachment of a security interest upon such Licensed Patents.

ARTICLE 9

LIGAND TO MAINTAIN CONFIDENTIALITY

9.1.1 Confidential Information . GSK shall be free to use without restriction or limitation any and all Confidential Information it has received or may receive from Ligand relating to the Licensed Assets as well as the terms of this Agreement. All Confidential Information that is jointly owned by the Parties (if any), the terms of this Agreement, all Confidential Information disclosed by GSK to Ligand during the term of this Agreement, and all Confidential Information relating in any way to the Licensed Assets

 

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(collectively, “ Confidential Information of GSK ”), in each case, shall be maintained as confidential by Ligand and shall not be used or disclosed by Ligand in any manner except as expressly permitted and contemplated (if at all) under this Agreement, except to the extent that the Confidential Information (as determined by competent documentation) either before or after the date of the disclosure to the other Party or its Affiliates becomes published or generally known to the public through no fault or omission on the part of the other Party, its Affiliates or its sublicensees. Specific information shall not be deemed to be within the foregoing exclusion merely because it is embraced by more general information falling within such exclusion.

9.2 Permitted Disclosure .

9.2.1 The provisions of Section 9.1 shall not preclude the other Party or its Affiliates from disclosing Confidential Information to the extent such Confidential Information is required to be disclosed by the other Party or its Affiliates to comply with applicable laws or court orders, to defend or prosecute litigation or to comply with governmental regulations, including the filing by Ligand of a redacted copy of this Agreement with the Securities and Exchange Commission, after prior review by GSK of such redacted copy, provided that the other Party provides prior written notice of such disclosure to the jointly-owning or disclosing Party and takes reasonable and lawful actions to avoid and/or minimize the degree of such disclosure.

9.2.2 Ligand shall have the right to disclose the material terms of this Agreement to any bona fide potential investor, investment banker, acquiror, merger partner or other potential financial partner. In connection with any permitted disclosure of Confidential Information pursuant to this Section 9.2.2, Ligand agrees to use all reasonable efforts to inform each disclosee of the confidential nature of such information and cause each disclosee to treat such information as confidential.

9.3 Employee and Advisor Obligations . Ligand agrees that it shall provide Confidential Information of GSK only to Ligand’s employees, consultants and advisors, and to the employees, consultants and advisors of Ligand’s Affiliates, who have a need to know and have an obligation to treat such information and materials as confidential.

9.4 Publications . GSK may publish or publicly disclose the results of any of the Development and Commercialization activities conducted hereunder related to the Licensed Compounds and/or Licensed Products.

9.5 Term . All obligations of confidentiality imposed under this Article 9 shall expire ten (10) years following termination or expiration of this Agreement.

ARTICLE 10

TERM AND TERMINATION

10.1 Term . This Agreement becomes effective as of the Effective Date and shall expire upon expiration of the Royalty Term.

 

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10.2 Termination . Prior to the expiration of this Agreement in accordance with its terms, Ligand shall have no right to terminate this Agreement or any right or obligation hereunder without obtaining the written consent of GSK. Prior to the expiration of this Agreement in accordance with its terms, GSK shall have the right to terminate this Agreement upon sixty (60) days notice to Ligand. In the event that a Party (the “ breaching Party ”) is in breach of any of its material obligations under this Agreement, then the other Party (the “ non-breaching Party ”) shall have the right to seek damages and such other remedies as may be available to it under law or in equity. Any such termination shall not relieve the terminating Party from obligations that have accrued prior to such termination or that expressly survive termination of this Agreement.

10.3 Survival . In the event of termination or expiration of this Agreement, the following provisions of this Agreement shall survive: Sections 2.1, 2.5, 4.1, 4.2, 6.1, 6.2, 6.3, 6.4 (for the time period set forth therein), 6.6, 6.7, 6.8, 6.9, 7.2 through 7.4 (but not following expiration of the Agreement) 7.5 (for the time period set forth therein), 7.6, 8.1, 8.8, 9 (for the time period set forth therein), 10, 11, 12 and 13.

ARTICLE 11

DISPUTE RESOLUTION

11.1 Dispute Resolution .

11.1.1 Executive Officers . Unless otherwise set forth in this Agreement, in the event of a dispute arising under this Agreement between the Parties, the Parties shall refer such dispute to the respective Executive Officers, and such Executive Officers shall attempt in good faith to resolve such dispute. For purposes of this subsection, “Executive Officers” means as to a Party, its chief executive officer (or such individual’s designee). If such position for either Party is vacant or does not exist, then the person having the most nearly equivalent position at such Party (or such individual’s designee) shall be deemed to be the Executive Officer of such Party.

11.1.2 Arbitration . If the Parties are unable to resolve a given dispute pursuant to Section 11.1.1 within [***] ([***]) days of referring such dispute to the Executive Officers, such dispute shall be resolved by binding arbitration in the manner described below:

(a) Arbitration Request . If a Party intends to begin an arbitration to resolve a dispute arising under this Agreement, such Party shall provide written notice (the “Arbitration Request”) to the other Party of such intention and the issues for resolution. From the date of the Arbitration Request and until such time as the dispute has become finally settled, the running of the time periods as to which Party must cure a breach of this Agreement becomes suspended as to the subject matter of the dispute. Unless the Parties otherwise agree in writing, during the period of time that any arbitration proceeding is pending under this Agreement, the Parties shall continue to comply with all those terms and provisions of this Agreement that are not the subject of the pending arbitration proceeding.

*** Certain information on this page has been omitted and filed separately with the Securities and Exchanged

Commission. Confidential treatment has been requested with respect to the omitted portions.

 

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(b) Additional Issues . Within ten (10) Business Days after the receipt of the Arbitration Request, the other Party may, by written notice, add additional issues for resolution.

(c) Arbitration Procedure . The arbitration shall be conducted by three (3) arbitrators who are knowledgeable in the subject matter at issue in the dispute. One (1) arbitrator will be selected by Ligand, one (1) arbitrator will be selected by GSK, and the third arbitrator will be selected by mutual agreement of the two (2) arbitrators selected by the Parties. The arbitration shall be held in Research Triangle Park, North Carolina under the rules of the American Arbitration Association if commenced by Ligand and in San Diego, California under the rules of the American Arbitration Association if commenced by GSK. The arbitrators may proceed to an award, notwithstanding the failure of either Party to participate in the proceedings. The arbitrators shall issue a written award and statement of decision describing the essential findings and conclusions on which the award is based, including the calculation of any damages awarded. The decision or award rendered by the Arbitrators shall be final and non-appealable, and judgment may be entered upon it in accordance with applicable law in the jurisdiction in which the arbitration has been held or any other court of competent jurisdiction. The arbitrators shall be authorized to award compensatory damages, but shall not be authorized to award non-economic damages or punitive damages, or to reform, modify or materially change this Agreement or any other agreements contemplated hereunder. The arbitrators also shall be authorized to grant any temporary, preliminary or permanent equitable remedy or relief the arbitrators deem just and equitable and within the scope of this Agreement, including an injunction or order for specific performance. The award of the arbitrators shall be the sole and exclusive remedy of the Parties. Judgment on the award rendered by the arbitrators may be enforced in any court having competent jurisdiction thereof, subject only to revocation on grounds of fraud or clear bias on the part of the arbitrators. Notwithstanding anything contained in this Section 11.3 to the contrary, each Party shall have the right to institute judicial proceedings against the other Party or anyone acting by, through or under such other Party, in order to preserve the status quo or to enforce the instituting Party’s rights hereunder through specific performance, injunction or similar equitable relief.

(d) Costs; Satisfaction . Each Party shall bear its own attorneys’ fees, costs, and disbursements arising out of the arbitration, and shall pay an equal share of the fees and costs of the arbitrators; provided , however, that the arbitrators shall be authorized to determine whether a Party is the prevailing Party, and if so, to award to that prevailing Party reimbursement for its reasonable attorneys’ fees, costs and disbursements (including, for example, expert witness fees and expenses, photocopy charges and travel expenses), and/or the fees and costs of the arbitrators. Absent the filing of an application to correct or vacate the arbitration award as permitted by applicable law, each Party shall fully perform and satisfy the arbitration award within fifteen (15) days of the service of the award with respect to payment obligations and within thirty (30) days of the service of the award with respect to other obligations (if any) imposed by the award.

11.2 Waiver . By agreeing to this binding arbitration provision, the Parties understand that they are waiving certain rights and protections which may otherwise be available if a dispute between the Parties were determined by litigation in court, including the right to seek or obtain certain types of damages precluded by this provision, the right to a jury trial, certain rights of appeal, and a right to invoke formal rules of procedure and evidence.

 

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11.3 Choice of Law . The validity, performance, construction and effect of this Agreement shall be governed by the laws of the State of New York, without regard to conflicts of law principles that would provide for application of the law of another jurisdiction. Notwithstanding the foregoing, any dispute, controversy or claim relating to the scope, validity, enforceability or infringement of any Patent Rights or other intellectual property rights shall be submitted to a court of competent jurisdiction in the territory in which such Patent Rights or other intellectual property rights were granted or arose.

ARTICLE 12

REPRESENTATIONS, WARRANTIES AND COVENANTS

12.1 Representation of Authority; Consents . Ligand and GSK each represents and warrants to the other Party that, as of the Execution Date, (a) it has full right, power and authority to enter into this Agreement, (b) this Agreement has been duly executed by such Party and constitutes a legal, valid and binding obligation of such Party, enforceable in accordance with its terms, except as enforceability may be limited by bankruptcy, fraudulent conveyance, insolvency, reorganization, moratorium and other laws relating to or affecting creditors’ rights generally and by general equitable principles and public policy constraints (including those pertaining to limitations and/or exclusions of liability, competition law, penalties and jurisdictional issues including conflicts of law) and (c) all necessary consents, approvals and authorizations of all government authorities and other persons required to be obtained by such Party in connection with the execution, delivery and performance of this Agreement have been and shall be obtained.

12.2 No Conflict . Each Party represents to the other Party that notwithstanding anything to the contrary in this Agreement, the execution and delivery of this Agreement and the performance of such Party’s obligations hereunder (a) do not conflict with or violate such Party’s corporate charter and bylaws or any requirement of applicable laws of regulations and (b) do not and shall not conflict with, violate or breach or constitute a default or require any consent under, any written contractual obligation of such Party. Each Party agrees that it shall not during the term of this Agreement grant any right, license, consent or privilege to any Third Party or otherwise undertake any action, either directly or indirectly, that would conflict with the rights granted to the other Party or interfere with any obligations of such Party set forth in this Agreement unless expressly permitted in this Agreement.

12.3 Grant of Rights . Ligand represents to GSK that it has sufficient legal and/or beneficial title, ownership or other rights to all of the Licensed Assets as is necessary to grant the licenses and rights to GSK that Ligand purports to grant to GSK pursuant to this Agreement.

12.4 Knowledge of Pending or Threatened Litigation . Each Party represents and warrants to the other Party that there is no claim, investigation, suit, action or proceeding pending or, to the knowledge of such Party, expressly threatened, against such Party before or by any governmental entity or arbitrator that, individually or in the aggregate, could reasonably be expected to (a) materially impair the ability of such Party to perform any obligation under this Agreement or (b) prevent or materially delay or alter the consummation of any or all of the transactions contemplated hereby.

 

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12.5 Intellectual Property; Other . Ligand represents and warrants that as of the Execution Date:

12.5.1 it has not received any written claim and it is not otherwise aware of any other claim, made against it asserting the invalidity, misuse, unregisterability, unenforceability or non-infringement of any of intellectual property rights associated with the Licensed Assets or challenging its right to use or ownership of any of the Licensed Assets or making any adverse claim of ownership thereof;

12.5.2 it is not aware of any pending or threatened claim or litigation which alleges that its activities up to the Execution Date relating to the Licensed Assets have violated, or by conducting the Development or Commercialization as currently proposed to be conducted hereunder would violate, the intellectual property rights of any Third Party;

12.5.3 the Licensed Patents include all of the Patent Rights relating to the Licensed Compounds, Licensed Products and/or thrombopoietin mimetics (a) which are owned by Ligand or its Affiliates, or (b) in which Ligand or its Affiliates have any interest or right, in each case other than any Patent Rights (if any) exclusively licensed to GSK under the Ligand/GSK Agreement;

12.5.4 Exhibit C sets forth a complete and correct list of the Licensed Patents as of the Execution Date;

12.5.5 it does not have any rights to or interests in any thrombopoietin mimetics which are in any state of development or regulatory approval, whether developed internally by Ligand, jointly with GSK or any other party or licensed from or to a Third Party, other than the Licensed Compounds and Licensed Products exclusively licensed to GSK under this Agreement and eltrombopag, for which Ligand receives milestones and royalties from GSK under the Ligand/GSK Agreement;

12.5.6 it does not have any rights to or interests in any products which are in any state of development or regulatory approval, whether developed internally by Ligand or jointly with GSK or any other party or licensed from or to a Third Party, where such products or the making, use, offering for sale, sale, or importation of such products is Covered by the Licensed Patents and which products are not included in the Licensed Products exclusively licensed to GSK under this Agreement;

12.5.7 no compounds being developed by Ligand in its G-CSF, EPO and interferon programs as of the Effective Date were identified by Ligand prior to 2002; and

12.5.8 no compounds being developed by Ligand in its G-CSF, EPO or interferon programs as of the Effective Date were designed using any compounds provided by GSK to Ligand under the Ligand/GSK Agreement and all such compounds being developed by Ligand are based upon screens conducted by Ligand after 2006 on Ligand’s chemical library.

 

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12.6 No Debarment . Each Party agrees it shall not knowingly use in connection with the Development or Commercialization under this Agreement any employee, consultant or investigator who is or has been debarred by a regulatory authority or who, to the best of such Party’s knowledge, is or has been the subject of debarment proceedings by a regulatory authority.

12.7 Existing Licensed Product . Ligand warrants that, at the time of delivery of the Existing Licensed Product to GSK: (a) such Existing Licensed Product will have been manufactured in accordance with cGMP and all applicable law; (b) such Existing Licensed Product will meet the Specifications and will conform with the Certificate of Analysis; (c) such Existing Licensed Product will not be adulterated or misbranded within the meaning of the FDCA; (d) title to such Existing Licensed Product will pass to GSK as provided herein free and clear of any security interest, lien or other encumbrance; (e) such Existing Licensed Product will have been manufactured in facilities that are in compliance with all applicable laws at the time of such manufacture (including applicable inspection requirements of FDA and other regulatory authorities); and (f) such Existing Licensed Product is not an article that may not be introduced into interstate commerce under the provisions of Sections 404 or 505 of the FDCA.

12.8 Disclaimer of Warranty . Nothing in this Agreement shall be construed as a representation made or warranty given by either Party that any patents will issue based on pending applications or that any such pending applications or patents issued thereon will be valid. EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, EACH PARTY EXPRESSLY DISCLAIMS, WAIVES, RELEASES AND RENOUNCES ANY WARRANTY, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.

ARTICLE 13

MISCELLANEOUS PROVISIONS

13.1 Indemnification .

13.1.1 GSK . GSK agrees to defend Ligand and its Affiliates at GSK’s cost and expense, and will indemnify and hold Ligand and its Affiliates and their respective directors, officers, employees and agents (the “ Ligand Indemnified Parties ”) harmless from and against any losses, costs, damages, fees or expenses arising out of any Third Party claim relating to (a) any breach by GSK of any of its representations, warranties or obligations pursuant to this Agreement, (b) the gross negligence or willful misconduct of GSK, (c) injuries resulting from the development, manufacture, use, sale or other disposition of any Licensed Compound or Licensed Product, or any other product or service offered by GSK, its Affiliates and/or its sublicensees or collaborators (other than Ligand), or (d) use by GSK of the Existing Licensed Compound. In the event of any such claim against the Ligand Indemnified Parties by any Third Party, Ligand shall promptly notify GSK in writing of the claim and GSK shall manage and control, at its sole expense, the defense of the claim and its settlement. The Ligand Indemnified Parties shall cooperate with GSK and may, at their option and expense, be represented in any such action or proceeding. GSK shall not be liable for any litigation costs or expenses incurred by the Ligand Indemnified Parties without GSK’s prior written authorization. In addition, GSK shall not be responsible for the

 

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indemnification or defense of any Ligand Indemnified Party to the extent arising from any negligent or intentional acts by any Ligand Indemnified Party or the breach by Ligand of any obligation or warranty under this Agreement, or any claims compromised or settled without its prior written consent.

13.1.2 Ligand . Ligand agrees to defend GSK and its Affiliates at Ligand’s cost and expense, and will indemnify and hold GSK and its Affiliates and their respective directors, officers, employees and agents (the “ GSK Indemnified Parties ”) harmless from and against any losses, costs, damages, fees or expenses arising out of any Third Party claim relating to (a) any breach by Ligand of any of its representations, warranties or obligations pursuant to this Agreement, (b) the gross negligence or willful misconduct of Ligand, (c) injuries resulting from any product or service offered by Ligand, its Affiliates and/or its licensees or collaborators (other than GSK); (d) injuries resulting from the Phase II Study conducted by Ligand pursuant to Section 2.3; or (e) any of the Ligand Liabilities. In the event of any claim against the GSK Indemnified Parties by any Third Party, GSK shall promptly notify Ligand in writing of the claim and Ligand shall manage and control, at its sole expense, the defense of the claim and its settlement. The GSK Indemnified Parties shall cooperate with Ligand and may, at their option and expense, be represented in any such action or proceeding. Ligand shall not be liable for any litigation costs or expenses incurred by the GSK Indemnified Parties without Ligand’s prior written authorization. In addition, Ligand shall not be responsible for the indemnification or defense of any GSK Indemnified Party to the extent arising from any negligent or intentional acts by any GSK Indemnified Party, or the breach by GSK of any obligation or warranty under this Agreement, or any claims compromised or settled without its prior written consent.

13.1.3 Insurance Proceeds . Any indemnification hereunder shall be made net of any insurance proceeds recovered by the Indemnified Party.

13.2 Insurance . GSK shall use all commercially reasonable efforts to maintain insurance, including product liability insurance, with respect to its activities hereunder. Such insurance shall be in such amounts and subject to such deductibles as the Parties may agree based upon standards prevailing in the industry at the time. GSK may satisfy its obligations under this Section through self-insurance to the same extent. At such time as a product is being manufactured by GSK for commercial sale, GSK shall name Ligand as an additional insured on any such policies. Any insurance shall not be construed to create a limit of GSK’s liability with respect to its indemnification obligations under Section 13.1 . GSK shall use commercially reasonable efforts to provide Ligand with written notice at least thirty (30) days prior to a cancellation, non-renewal or material change in such insurance or self-insurance that could materially adversely affect the rights of Ligand hereunder. GSK’s insurance hereunder shall be primary and non-contributing.

13.3 Assignment . GSK may, in whole or in part, delegate, assign and/or sublicense to any of its Affiliates or sublicensees any or all of the rights and/or obligations GSK has under this Agreement. Further, GSK may assign this Agreement, in whole or in part, in connection with any sale or transfer (by merger or otherwise) of any businesses, assets or products owned or Controlled by GSK, provided that the acquirer confirms to Ligand in writing its agreement to be bound by all of the terms and conditions of this Agreement. Ligand may not assign, nor delegate any obligation under this Agreement, in whole or in part, without first obtaining the prior written consent of GSK, except in connection with any sale or transfer (by merger or otherwise) to a Third Party of all of the

 

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business or assets owned or Controlled by Ligand, in which case GSK’s prior written consent shall not be required; provided , however, that the acquirer or assignee confirms to GSK in writing its agreement to be bound by all of the terms and conditions of this Agreement. Any purported assignment not in accordance with this Section 13.3 shall be void and of no effect.

13.4 Entire Agreement; Amendments . This Agreement and the Schedules referred to in this Agreement constitute the entire agreement between the Parties with respect to the subject matter hereof, and supersede all previous arrangements with respect to the subject matter hereof, whether written or oral. Any amendment or modification to this Agreement shall be made in writing signed by both Parties. No trade customs, courses of dealing or courses of performance by the Parties will be relevant to modify, supplement or explain any term(s) used in this Agreement. This Agreement may not be modified or supplemented by any purchase order, change order, acknowledgement, order acceptance, standard terms of sale, invoice or the like.

13.5 Notices .

Notices to Ligand shall be addressed to:

Ligand Pharmaceuticals Incorporated.

10275 Science Center Drive

San Diego, CA 92121

Attention: General Counsel

Facsimile No.: (858) 550-7272

Notices to GSK shall be addressed to:

SmithKline Beecham Corporation, d/b/a GlaxoSmithKline

One Franklin Plaza

Philadelphia, PA 19101

Attn: Senior Vice President, Worldwide Business Development

Facsimile: (610) 270-5166

with a required copy to:

SmithKline Beecham Corporation, d/b/a GlaxoSmithKline

2301 Renaissance Boulevard

King of Prussia, PA 19406-2772

Vice President and Associate General Counsel, R&D Legal Operations

Facsimile: (610) 787-7084

Either Party may change its address to which notices shall be sent by giving notice to the other Party in the manner herein provided. Any notice required or provided for by the terms of this Agreement shall be in writing and shall be (a) sent by registered or certified mail, return receipt requested, postage prepaid, (b) sent via a reputable overnight courier service, or (c) sent by facsimile transmission, in each case properly addressed in accordance with this Section 13.5. The effective date of notice shall be the actual date of receipt by the Party receiving the same.

 

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CONFIDENTIAL

EXECUTION VERSION

 

13.6 Force Majeure . No failure or omission by either Party in the performance of any obligation of this Agreement shall be deemed a breach of this Agreement or create any liability if the same shall arise from any cause or causes beyond the control of such Party, including, but not limited to, the following: acts of gods; acts of any government; any rules, regulations or orders issued by any governmental authority or by any officer, department, agency or instrumentality thereof; fire; storm; flood; earthquake; accident; war; rebellion; insurrection; riot; terrorism and invasion; provided that the Party affected by such cause promptly notifies the other Party and uses reasonable efforts to cure such failure or omission as soon as is practicable after the occurrence of one or more of the above mentioned causes.

13.7 Compliance with Export Regulations . Neither Party shall export any technology licensed to it by the other Party under this Agreement except in compliance with U.S. export laws and regulations.

13.8 Public Announcements . On the Execution Date, the Parties may issue one or more press releases, the timing and content of which shall be mutually agreed. Any announcements or similar publicity with respect to the execution of this Agreement shall be agreed upon between the Parties in advance of such announcement. The Parties understand that this Agreement is likely to be of significant interest to investors, analysts and others, and that the Parties therefore may make such public announcements with respect thereto, subject to the remainder of this Section 13.8. The Parties agree that any such announcement will not contain confidential business or technical information and, if disclosure of confidential business or technical information is required by law or regulation, the Parties will use commercially reasonable efforts to minimize such disclosure and obtain confidential treatment for any such information which is disclosed to a governmental agency or group; provided that Ligand shall have the right to disclose the financial terms contained in this Agreement, including the milestones and royalty rates, without the agreement in advance of GSK. Each Party agrees to provide to the other Party a copy of any public announcement as soon as reasonably practicable under the circumstances prior to its scheduled release. Except under extraordinary circumstances, each Party shall provide the other with an advance copy of any press release at least five (5) days prior to the scheduled disclosure. Each Party shall have the right to expeditiously review and recommend changes to any announcement regarding this Agreement or the subject matter of this Agreement. Except as otherwise required by law, the Party whose press release has been reviewed shall remove any information the reviewing Party reasonably deems to be inappropriate for disclosure. The contents of any such announcement or similar publicity which has been reviewed and approved by the reviewing Party can be re-released by either Party without a requirement for re-approval. Furthermore, each Party shall give the other Party a reasonable opportunity to review all filings with the United States Securities and Exchange Commission describing the terms of this Agreement prior to submission of such filings, and shall give due consideration to any reasonable comments by the non-filing Party relating to such filing, including without limitation the provisions of this Agreement for which confidential treatment should be sought. Neither Party hereto shall use the name, trademarks, logos, physical likeness, employee names or owner symbol of the other Party for any promotional, advertising, marketing or commercial activities without the prior written consent of the other Party.

 

30


CONFIDENTIAL

EXECUTION VERSION

 

13.9 Relationship Between the Parties . It is understood and agreed that the relationship between the Parties is that of independent contractors and that nothing in this Agreement shall be construed as authorization for either Ligand or GSK to act as agent for the other. Further, nothing in this Agreement is intended or shall be deemed to constitute a partnership or joint venture relationship between the Parties. No Party shall incur any debts or make any commitments for the other(s), except to the extent, if at all, specifically provided under this Agreement.

13.10 Headings . The captions or headings of the sections or other subdivisions hereof are inserted only as a matter of convenience or for reference and shall have no effect on the meaning of the provisions hereof.

13.11 Joint Preparation . The language in all parts of this Agreement shall be deemed to be the language mutually chosen by the Parties. The Parties and their counsel have cooperated in the drafting and preparation of this Agreement, and this Agreement therefore shall not be construed against any Party by virtue of its role as the drafter thereof. No drafts of this Agreement or any other similar or related document exchanged by the Parties prior to the Execution Date shall be offered by a Party, nor shall any draft be admissible in any proceeding, to explain or construe this Agreement or for any other purpose.

13.12 No Implied Waivers; Rights Cumulative . No failure on the part of Ligand or GSK to exercise, and no delay by either Party in exercising, any right, power, remedy or privilege under this Agreement, or provided by statute or at law or in equity or otherwise, shall impair, prejudice or constitute a waiver of any such right, power, remedy or privilege by such Party or be construed as a waiver of any breach of this Agreement or as an acquiescence therein by such Party, nor shall any single or partial exercise of any such right, power, remedy or privilege by a Party preclude any other or further exercise thereof or the exercise of any other right, power, remedy or privilege.

13.13 Severability . To the fullest extent permitted by applicable law, the Parties waive any provision of law that would render any provision in this Agreement invalid, illegal or unenforceable in any respect. If any provision of this Agreement is held to be invalid, illegal or unenforceable, in any respect or to any extent, then in such respect and to such extent such provision will be given no effect by the Parties and shall not form part of this Agreement. To the fullest extent permitted by applicable law, all other provisions of this Agreement shall remain in full force and effect and the Parties will use commercially reasonable efforts to negotiate a provision in replacement of the provision held invalid, illegal or unenforceable that is consistent with applicable law and achieves, as nearly as possible, the original intention of the Parties.

13.14 Execution in Counterparts . This Agreement may be executed in counterparts, each of which counterparts, when so executed and delivered, shall be deemed to be an original, and all of which counterparts, taken together, shall constitute one and the same instrument.

 

31


CONFIDENTIAL

EXECUTION VERSION

 

13.15 No Third Party Beneficiaries . No person or entity other than GSK, Ligand and their respective Affiliates and permitted assignees hereunder shall be deemed an intended beneficiary hereunder or have any right to enforce any obligation of this Agreement.

13.16 No Consequential Damages . UNLESS RESULTING FROM A PARTY’S GROSS NEGLIGENCE OR WILLFUL MISCONDUCT, NEITHER PARTY HERETO WILL BE LIABLE FOR SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THIS AGREEMENT OR THE EXERCISE OF ITS RIGHTS HEREUNDER, INCLUDING WITHOUT LIMITATION LOST PROFITS ARISING FROM OR RELATING TO ANY BREACH OF THIS AGREEMENT, REGARDLESS OF ANY NOTICE OF SUCH DAMAGES. NOTHING IN THIS SECTION 13.16 IS INTENDED TO LIMIT OR RESTRICT THE INDEMNIFICATION RIGHTS OR OBLIGATIONS OF EITHER PARTY UNDER SECTION 13.1 , OR DAMAGES AVAILABLE FOR BREACHES OF CONFIDENTIALITY OBLIGATIONS IN ARTICLE 9 .

[Signature page follows]

 

32


CONFIDENTIAL

EXECUTION VERSION

 

IN WITNESS WHEREOF, the Parties have executed this License Agreement as of the Execution Date.

 

L IGAND P HARMACEUTICALS I NCORPORATED
By:   /s/ John L. Higgins
Title:   Chief Executive Officer
S MITH K LINE B EECHAM C ORPORATION D / B / A G LAXO S MITH K LINE
By:   /s/ William J. Mosher
Title:   Assistant Secretary

 

33


List of Exhibits :

 

Exhibit A    Certificate of Analysis
Exhibit B    LGD-4665, its molecular structure and disclosure of any other thrombopoietin mimetics discovered or developed by or behalf of Ligand
Exhibit C    Licensed Patents
Exhibit D    Amount of bulk and finished Existing Licensed Compound
Exhibit E    Existing Regulatory Filings
Exhibit F    Licensed Know-How from Data Room to be Transferred to GSK


CONFIDENTIAL

EXECUTION VERSION

 

Exhibit A

Certificate of Analysis

LOGO

 

LIGAND PHARMACEUTICALS INC.

DATE:

  

ANALYTICAL DEVELOPMENT

SUPERSEDES:

SUPERSEDES DATE:

TESTING SUMMARY

DOCUMENT NUMBER:

 

DRUG PRODUCT:

LIGAND LOT NUMBER:

CARDINAL LOT NUMBER:

PLACE OF MANUFACTURE:

MONOGRAPH NUMBER:

SPECIFICATION NUMBER:

TESTING FACILITY:

  

DATE OF MANUFACTURE:

RE-TEST DATE:

 

 

TEST

  

SPECIFICATION LIMITS

  

RESULT

PHYSICAL DESCRIPTION      
Identification by HPLC      
Identification by UV      
Dissolution      
Content Uniformity      
HPLC ASSAY      
INDIVIDUAL RELATED SUBSTANCES      
TOTAL RELATED SUBSTANCES      

WATER CONTENT

    (Karl Fischer)

     

 

35


CONFIDENTIAL

EXECUTION VERSION

 

TESTING SUMMARY

DOCUMENT NUMBER:

DRUG PRODUCT :

LIGAND LOT NUMBER :

CARDINAL LOT NUMBER :

DOCUMENT NUMBER :

DATE :

Total aerobic microbial

count (Total Plate Count)

Total combined mold &

yeast count

Escherichia coli

Salmonella Species

Staphylococcus aureus

Pseudomonas aeruginosa

REVIEWED/APPROVED BY :

 

                    
Analytical Development     Date          Date

 

36


CONFIDENTIAL

EXECUTION VERSION

 

Exhibit B

Molecular structure of LGD-4665 and disclosure of any other thrombopoietin mimetics discovered or developed by or on behalf of Ligand

[***]

Structures and/or names of other thrombopoietin mimetics discovered or developed by or on behalf of Ligand set forth in the patents and applications listed on Exhibit C are incorporated herein by reference.

*** Certain information on this page has been omitted and filed separately with the Securities and Exchanged Commission. Confidential treatment has been requested with respect to the omitted portions.

 

37


CONFIDENTIAL

EXECUTION VERSION

 

Exhibit C

Licensed Patents

[***]

 

Country

 

App. No.

 

Filing Date

 

Patent No.

 

Date Issued

 

Pub No.

 

Pub Date

[***]   [***]   [***]       [***]   [***]
[***]   [***]   [***]     [***]    
[***]   [***]   [***]     [***]   [***]   [***]
[***]   [***]   [***]   [***]   [***]   [***]   [***]
[***]   [***]   [***]       [***]   [***]
[***]   [***]   [***]       [***]   [***]
[***]   [***]   [***]     [***]    
[***]   [***]   [***]     [***]    
[***]   [***]   [***]       [***]   [***]
[***]   [***]   [***]        
[***]   [***]   [***]         [***]
[***]   [***]   [***]        
[***]   [***]   [***]       [***]   [***]
[***]   [***]   [***]        
[***]   [***]   [***]        
[***]   [***]   [***]        
[***]   [***]   [***]       [***]   [***]
[***]   [***]   [***]        
[***]   [***]   [***]        
[***]   [***]   [***]        
[***]   [***]   [***]        
[***]   [***]   [***]     [***]   [***]   [***]
[***]   [***]   [***]        
[***]   [***]   [***]        
[***]   [***]   [***]        
[***]   [***]   [***]     [***]    
[***]   [***]   [***]     [***]    
[***]   [***]   [***]       [***]   [***]
[***]   [***]   [***]        
[***]     [***]        
[***]     [***]        
[***]   [***]   [***]        
[***]   [***]   [***]       [***]   [***]
[***]   [***]   [***]        
[***]   [***]   [***]        
[***]     [***]        
[***]   [***]   [***]        

*** Certain information on this page has been omitted and filed separately with the Securities and Exchanged Commission. Confidential treatment has been requested with respect to the omitted portions.

 

38


CONFIDENTIAL

EXECUTION VERSION

 

Country

 

App. No.

 

Filing Date

 

Patent No.

 

Date Issued

 

Pub No.

 

Pub Date

[***]   [***]   [***]        
[***]   [***]   [***]        
[***]   [***]   [***]       [***]   [***]
[***]   [***]   [***]        
[***]   [***]   [***]     [***]    
[***]   [***]   [***]        
[***]     [***]        
[***]     [***]        
[***]     [***]        
[***]   [***]   [***]        
[***]     [***]        
[***]   [***]   [***]        
[***]     [***]        
[***]   [***]   [***]        
[***]   [***]   [***]        
[***]   [***]   [***]        
[***]   [***]   [***]       [***]   [***]
[***]   [***]   [***]        
[***]   [***]   [***]        

*** Certain information on this page has been omitted and filed separately with the Securities and Exchanged Commission. Confidential treatment has been requested with respect to the omitted portions.

 

39


CONFIDENTIAL

EXECUTION VERSION

 

Exhibit D

Amount of bulk and finished Existing Licensed Compound

Non-GMP API: Approximately [***] kg. [***] kilograms are stored at -70C at Ligand and about [***] kg of non-GMP API is stored at -20C at Fisher Clinical Services.

GMP API: About [ *** ] kg of GMP API is stored at Fisher Clinical Services.

*** Certain information on this page has been omitted and filed separately with the Securities and Exchanged Commission. Confidential treatment has been requested with respect to the omitted portions.

 

40


CONFIDENTIAL

EXECUTION VERSION

 

Exhibit E

Existing Regulatory Filings

LGD4665 [***]

LGD4665 [***]

*** Certain information on this page has been omitted and filed separately with the Securities and Exchanged Commission. Confidential treatment has been requested with respect to the omitted portions.

 

41


CONFIDENTIAL

EXECUTION VERSION

 

Exhibit F

Licensed Know-How from Data Room to be Transferred to GSK

[***]

*** Certain information on this page has been omitted and filed separately with the Securities and Exchanged Commission. Confidential treatment has been requested with respect to the omitted portions.

 

42

Exhibit 23.1

CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

We have issued our reports dated March 13, 2009, with respect to the consolidated financial statements, schedule, and internal control over financial reporting included in the Annual Report of Ligand Pharmaceuticals Incorporated on Form 10-K for the year ended December 31, 2008. We hereby consent to the incorporation by reference of said report in the Registration Statements of Ligand Pharmaceuticals Incorporated on Form S-8 (File No. 333-131029, effective June 18, 2007).

/s/ Grant Thornton LLP

San Diego, California

March 13, 2009

Exhibit 23.2

CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

Ligand Pharmaceuticals Incorporated

San Diego, California

We hereby consent to the incorporation by reference in the Registration Statement on Form S-8 No. 333-131029 of Ligand Pharmaceuticals Incorporated of our report dated February 28, 2008, relating to the consolidated financial statements which is incorporated by reference in this Annual Report on Form 10-K. We also consent to the incorporation by reference of our report dated February 28, 2008 relating to the financial statement schedule, which appears in this Form 10-K.

/s/ BDO Seidman, LLP

San Diego, California

March 13, 2009

Exhibit 31.1

CERTIFICATION OF PRINCIPAL EXECUTIVE OFFICER

PURSUANT TO EXCHANGE ACT RULE 13a-14(a)/15d-14(a)

AS ADOPTED PURSUANT TO SECTION 302 OF THE SARBANES-OXLEY ACT OF 2002

I, John L. Higgins, certify that:

1. I have reviewed this Annual Report on Form 10-K of Ligand Pharmaceuticals Incorporated;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) designed such internal control over financial reporting, or caused such control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting.

5. The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a) all significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b) any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: March 13, 2009

 

/s/    J OHN L. H IGGINS        

John L. Higgins
President, Chief Executive Officer and Director
(Principal Executive Officer)

Exhibit 31.2

CERTIFICATION OF PRINCIPAL FINANCIAL OFFICER

PURSUANT TO EXCHANGE ACT RULE 13a-14(a)/15d-14(a)

AS ADOPTED PURSUANT TO SECTION 302 OF THE SARBANES OXLEY-ACT OF 2002

I, John P. Sharp, certify that:

1. I have reviewed this Annual Report on Form 10-K of Ligand Pharmaceuticals Incorporated;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) designed such internal control over financial reporting, or caused such control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting.

5. The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a) all significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b) any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: March 13, 2009

 

/s/    J OHN P. S HARP        

John P. Sharp
Vice President, Finance and Chief Financial Officer
(Principal Financial Officer)

Exhibit 32.1

CERTIFICATION BY PRINCIPAL EXECUTIVE OFFICER

PURSUANT TO 18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO SECTION 906

OF THE SARBANES-OXLEY ACT OF 2002

In connection with the accompanying Annual Report on Form 10-K of Ligand Pharmaceuticals Incorporated (the “Company”) for the year ended December 31, 2008, I, John L. Higgins, President, Chief Executive Officer and Director of the Company, hereby certify pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, to the best of my knowledge and belief, that:

(1) such Annual Report on Form 10-K for the year ended December 31, 2008, fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended; and

(2) the information contained in such Annual Report on Form 10-K for the year ended December 31, 2008, fairly presents, in all material respects, the financial condition and results of operations of the Company.

The foregoing certification is being furnished solely to accompany such Annual Report on Form 10-K for the year ended December 31, 2008, pursuant to 18 U.S.C. § 1350, and is not being filed for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, and is not to be incorporated by reference into any filing of the Company, whether made before or after the date hereof, regardless of any general incorporation language in such filing.

 

Date: March 13, 2009  

/s/    J OHN L. H IGGINS        

 

John L. Higgins

President, Chief Executive Officer and Director

(Principal Executive Officer)

Exhibit 32.2

CERTIFICATION BY PRINCIPAL FINANCIAL OFFICER

PURSUANT TO 18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO SECTION 906

OF THE SARBANES-OXLEY ACT OF 2002

In connection with the accompanying Annual Report on Form 10-K of Ligand Pharmaceuticals Incorporated (the “Company”) for the year ended December 31, 2008, I, John P. Sharp, Vice President, Finance and Chief Financial Officer of the Company, hereby certify pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, to the best of my knowledge and belief, that:

(1) such Annual Report on Form 10-K for the year ended December 31, 2008, fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended; and

(2) the information contained in such Annual Report on Form 10-K for the year ended December 31, 2008, fairly presents, in all material respects, the financial condition and results of operations of the Company.

The foregoing certification is being furnished solely to accompany such Annual Report on Form 10-K for the year ended December 31, 2008, pursuant to 18 U.S.C. § 1350, and is not being filed for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, and is not to be incorporated by reference into any filing of the Company, whether made before or after the date hereof, regardless of any general incorporation language in such filing.

 

Date: March 13, 2009  

/s/    J OHN P. S HARP        

 

John P. Sharp

Vice President, Finance and Chief Financial Officer

(Principal Financial Officer)