8-K

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d) of the

Securities Exchange Act of 1934

Date of Report (Date of earliest event reported): September 25, 2009

LIGAND PHARMACEUTICALS INCORPORATED

(Exact Name of Registrant as Specified in Its Charter)

Delaware	001-33093	77-0160744
(State or Other Jurisdiction of Incorporation or Organization)	(Commission File Number)	(I.R.S. Employer Identification No.)

10275 Science Center Drive, San Diego, California, 92121-1117

(Address of Principal Executive Offices) (Zip Code)

(858) 550-7500

(Registrant’s Telephone Number, Including Area Code)

N/A

(Former Name or Former Address, if Changed Since Last Report)

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:

¨ Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)

¨ Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)

¨ Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))

¨ Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))

Item 1.01. Entry Into a Material Definitive Agreement.

On September 25, 2009, Pharmacopeia, LLC (“Pharmacopeia”), a wholly owned subsidiary of Ligand Pharmaceuticals Incorporated (together with Pharmacopeia, the “Company” or “Ligand”), entered into an amendment (the “Amendment”) to its product development and commercialization agreement dated March 24, 2006 (the “Product Development Agreement”) with SmithKline Beecham Corporation, doing business as GlaxoSmithKline, and Glaxo Group Limited (together, “GSK”). Pursuant to the terms of the Amendment, Ligand and GSK agreed to terminate three research and development programs and their associated targets under the Product Development Agreement and to immediately terminate their respective exclusivity obligations with respect to two programs and their associated targets. The three programs to be terminated will be mutually agreed by Ligand and GSK within sixty days of the date of the Amendment. In addition, in the event that GSK does not exercise its option with respect to the two additional programs as to which exclusivity obligations are terminated, all rights to any such program will revert to Ligand. Ligand will be free to pursue research, development or commercialization of the three terminated or reverted programs without restriction; GSK will remain subject to specified obligations of exclusivity for such programs for a limited period of time. Ligand and GSK also agreed to accelerate the timing of a $500,000 payment to the Company that would otherwise be required upon identification a new lead compound for advancement under the Product Development Agreement.

The foregoing description of the Amendment does not purport to be complete and is qualified in its entirety by reference to the Amendment, a copy of which the Company intends to file with its Quarterly Report on Form 10-Q for the quarter ending September 30, 2009, requesting confidential treatment for certain portions.

Item 7.01 Regulation FD Disclosure.

In connection with the announcement by Ligand that it has earned the payment described in Item 1.01 of this Current Report on Form 8-K, the Company issued a press release on September 28, 2009. A copy of this press release is included as Exhibit 99.1 to this Current Report on Form 8-K and is incorporated herein by reference.

In accordance with General Instruction B.2. of Form 8-K, the information in this Item 7.01 of this Current Report on Form 8-K, including Exhibit 99.1, shall not be deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference in any filing under the Securities Act of 1933, as amended, or the Exchange Act, except as expressly set forth by specific reference in such a filing.

Item 9.01 Financial Statements and Exhibits.

(d) Exhibits.

Exhibit No.	Description
99.1*	Press Release of the Company dated September 28, 2009.

* The information in Exhibit 99.1 to this Current Report on Form 8-K shall not be deemed “filed” for purposes of Section 18 of the Exchange Act, or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference in any filing under the Securities Act or the Exchange Act, except as expressly set forth by specific reference in such a filing.

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, the registrant has caused this report to be signed on its behalf by the undersigned.

	LIGAND PHARMACEUTICALS INCORPORATED
Date: October 1, 2009	By:	/s/    CHARLES S. BERKMAN
	Name:	Charles S. Berkman
	Title:	Vice President, General Counsel and Secretary

EXHIBIT INDEX

Exhibit No.	Description
99.1*	Press Release of the Company dated September 28, 2009.

* The information in Exhibit 99.1 to this Current Report on Form 8-K shall not be deemed “filed” for purposes of Section 18 of the Exchange Act, or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference in any filing under the Securities Act or the Exchange Act, except as expressly set forth by specific reference in such a filing.

EX-99.1

Exhibit 99.1

Contacts:

Ligand Pharmaceuticals Incorporated Lippert/Heilshorn & Associates

John L. Higgins, President and CEO or Don Markley

Erika Luib, Investor Relations dmarkley@lhai.com

(858) 550-7896 (310) 691-7100

Ligand and GlaxoSmithKline Collaboration Identifies New Compound

Ligand Earns Milestone Payment and Amends Agreement with GlaxoSmithKline

SAN DIEGO, Sep 28, 2009 (BUSINESS WIRE) — Ligand Pharmaceuticals Incorporated (NASDAQ:LGND) today announced that pursuant to an amendment to a March 2006 research agreement with GlaxoSmithKline (NYSE:GSK), GSK has agreed to accelerate the timing of a $500,000 payment to Ligand that would otherwise have been required upon the identification of a new lead chemical series for advancement in its alliance with GSK. This chemical series is from a program being evaluated as a potential treatment for inflammatory indications identified through the collaboration. Including this milestone, Ligand has earned a total of $4 million from GSK in connection with the discovery of eight new leads in the collaboration.

In addition, under the amended agreement Ligand and GSK agreed to waive exclusivity on two biological targets, allowing both GSK and Ligand the freedom to pursue independent research programs with such targets in addition to the current alliance programs. Furthermore, pursuant to the amended agreement Ligand will gain full research, development and/or commercialization rights to certain targets and back-up compounds associated with the drug-screening collaboration.

Under the amended agreement, Ligand remains entitled to receive success-based milestone payments from GSK, starting in the preclinical research stage, for each drug development program and potentially up to double-digit royalties on the sales of any product commercialized by GSK under the multi-program alliance.

About Ligand Pharmaceuticals

Ligand discovers and develops new drugs that address critical unmet medical needs of patients with muscle wasting, frailty, hormone-related diseases, osteoporosis, inflammatory diseases, anemia, asthma, rheumatoid arthritis and psoriasis. Ligand’s proprietary drug discovery and development programs are based on advanced cell-based assays, gene-expression tools, ultra-high throughput screening and one of the world’s largest combinatorial chemical libraries. Ligand has strategic alliances with major pharmaceutical and biotechnology companies, including Bristol-Myers Squibb, Celgene, Cephalon, GlaxoSmithKline, Schering-Plough, Pfizer and Wyeth Pharmaceuticals. With nine pharmaceutical agreements and more than 20 molecules in various stages of development, Ligand utilizes proprietary technologies for identifying drugs with novel receptor and enzyme drug targets.

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Caution Regarding Forward-Looking Statements

This news release contains forward-looking statements by Ligand that involve risks and uncertainties and reflect Ligand’s judgment as of the date of this release. These statements include those regarding timing and results of clinical data for the GSK program, data analysis and evaluation of compounds or related product candidates utility or potential benefits to patients, the potential commercial market and plans for continued development and further studies of the compounds and other related product candidates. Actual events or results may differ from Ligand’s expectations. For example, there can be no assurance that other trials or evaluations of these compounds and other related product candidates will be favorable or that they will confirm results of previous studies, that data evaluation will be completed or demonstrate any hypothesis or endpoint, that we will receive any milestone payments in the future, that the compounds and other related product candidates will provide utility or benefits to certain patients, that any presentations will be favorably received, or that clinical or commercial development of these compounds or related product candidates will be initiated, completed or successful or that our rights to these compounds and other related product candidates will not be successfully challenged. The failure to meet expectations with respect to any of the foregoing matters may reduce Ligand’s stock price. Additional information concerning these and other risk factors affecting Ligand can be found in prior press releases available at www.ligand.com as well as in public periodic filings with the Securities and Exchange Commission, available via www.sec.gov. Ligand disclaims any intent or obligation to update these forward-looking statements beyond the date of this press release. This caution is made under the safe harbor provisions of the Private Securities Litigation Reform Act of 1995.

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