1 SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-K/A AMENDMENT NO. 1 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, 1997, OR [ ] TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD COMMISSION FILE NUMBER: 0-20720 FROM ______ TO _______. LIGAND PHARMACEUTICALS INCORPORATED (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER) DELAWARE 77-0160744 (STATE OF OTHER JURISDICTION OF (I.R.S. EMPLOYER INCORPORATION OR ORGANIZATION) IDENTIFICATION NO.) 10275 SCIENCE CENTER DRIVE 92121-1117 SAN DIEGO, CA (ZIP CODE) (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES) REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE: (619) 550-7500 SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT: NONE SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT: COMMON STOCK, $.001 PAR VALUE WARRANTS TO PURCHASE ONE SHARE OF COMMON STOCK, $.001 PAR VALUE PREFERRED SHARE PURCHASE RIGHTS 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. [ ] The aggregate market value of the Registrant's voting stock held by non-affiliates as of February 28, 1998 was $488,205,375. For purposes of this calculation, shares of Common Stock held by directors, officers and 5% stockholders known to 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 28, 1998 the registrant had 38,594,979 shares of Common Stock outstanding. 2 EXPLANATORY NOTE This Annual Report on Form 10-K/A for the fiscal year ended December 31, 1997 is being filed solely to refile a new version of Exhibits 10.169 and 10.172 hereto (pursuant to a confidential treatment request filed with the Securities and Exchange Commission (the "Commission")) and to amend the list of Exhibits and the Exhibit Index included herein relating thereto. The 10-K/A constitutes Amendment No. 1 to Ligand Pharmaceuticals Incorporated's Annual report on Form 10-K for the fiscal year ended December 31, 1997. PART IV ITEM 14. EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS ON FORM 8-K (c) EXHIBITS. EXHIBIT NO. DESCRIPTION -------- ----------- # 2.1 Agreement of Merger, dated February 7, 1995 by and among Ligand Pharmaceuticals Incorporated, LG Acquisition Corp. and Glycomed Incorporated (other Exhibits omitted, but will be filed by the Company with the Commission upon request). # 2.2 Form of Plan of Merger. # 3.2 Amended and Restated Certificate of Incorporation of the Company. & 3.3 Bylaws of the Company, as amended. X 3.4 Certificate of Designation of Rights, Preferences and Privileges of Series A Participating Preferred Stock of Ligand Pharmaceuticals Incorporated. (Exhibit 3.1). * 4.1 Specimen stock certificate for shares of Common Stock of the Company. # 10.1 The Company's 1992 Stock Option/Stock Issuance Plan, as amended. * 10.2 Form of Stock Option Agreement. * 10.3 Form of Stock Issuance Agreement. * 10.7 The Company's 1988 Stock Option Plan, as amended. * 10.8 Form of Incentive Stock Option Agreement (Installment Vesting). * 10.9 Form of Non-Qualified Stock Option Agreement (Installment Vesting). * 10.10 Form of Consultant Non-Qualified Stock Option Agreement (Immediate Vesting). * 10.12 1992 Employee Stock Purchase Plan. * 10.13 Form of Stock Purchase Agreement. * 10.29 Consulting Agreement, dated October 20, 1988, between the Company and Dr. Ronald M. Evans, as amended by Amendment to Consulting Agreement, dated August 1, 1991, and Second Amendment to Consulting Agreement, dated March 6, 1992. * 10.30 Form of Proprietary Information and Inventions Agreement. Research and License. * 10.31 Agreement, dated March 9, 1992, between the Company and Baylor College of Medicine (with certain confidential portions omitted). * 10.33 License Agreement, dated November 14, 1991, between the Company and Rockefeller University (with certain confidential portions omitted). * 10.34 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 Agreement, dated May 1, 1991, between the Company and Pfizer Inc (with certain confidential portions omitted). * 10.36 License Agreement, dated July 3, 1990, between the Company and the Brigham and Woman's Hospital, Inc. (with certain confidential portions omitted). * 10.37 Compound Evaluation Agreement, dated May 17, 1990, between the Company and SRI International (with certain confidential portions omitted). * 10.38 License Agreement, dated January 5, 1990, between the Company and the University of North Carolina at Chapel Hill (with certain confidential portions omitted). * 10.40 License Agreement, dated January 4, 1990, between the Company and Baylor College of Medicine (with certain confidential portions omitted). * 10.41 License Agreement, dated October 1, 1989, between the Company and Institute Pasteur (with certain confidential portions omitted). * 10.42 Sublicense Agreement, dated September 13, 1989, between the Company and AndroBio Corporation (with certain confidential portions omitted). 3 EXHIBIT NO. DESCRIPTION -------- ----------- * 10.43 License Agreement, dated June 23, 1989, between the Company and La Jolla Cancer Research Foundation (with certain confidential portions omitted). * 10.44 License Agreement, dated October 20, 1988, between the Company and the Institute for Biological Studies, as amended by Amendment to License Agreement dated September 15, 1989, Second Amendment to License Agreement, dated December 1, 1989 and Third Amendment to License Agreement dated October 20, 1990 (with certain confidential portions omitted). * 10.45 Agreement dated June 12, 1989, between the Company and the Regents of the University of California. * 10.46 Form of Indemnification Agreement between the Company and each of its directors. * 10.47 Form of Indemnification Agreement between the Company and each of its officers. * 10.50 Consulting Agreement, dated October 1, 1991, between the Company and Dr. Bert W. O'Malley. * 10.53 Stock And Warrant Purchase Agreement, Dated June 30, 1992 Between The Company And Allergan, Inc. And Allergan Pharmaceuticals (Ireland) Ltd., Inc. * 10.58 Stock Purchase Agreement, dated September 9, 1992, between the Company and Glaxo, Inc. * 10.59 Research and Development Agreement, dated September 9, 1992, between the Company and Glaxo, Inc. (with certain confidential portions omitted). * 10.60 Stock Transfer Agreement, dated September 30, 1992, between the Company and the Rockefeller University. * 10.61 Stock Transfer Agreement, dated September 30, 1992, between the Company and New York University. * 10.62 License Agreement, dated September 30, 1992, between the Company and the Rockefeller University (with certain confidential portions omitted). * 10.63 Professional Services Agreement, dated September 30, 1992, between the Company and Dr. James E. Darnell. * 10.64 Letter Agreement, dated August 24, 1992, between the Company and Dr. Howard T. Holden. * 10.65 Letter Agreement, dated August 20, 1992, between the Company and Dr. George Gill. * 10.66 Letter Agreement, dated September 3, 1992, between the Company and Dr. Lloyd E. Flanders. * 10.67 Letter Agreement, dated September 11, 1992, between the Company and Mr. Paul Maier. !! 10.69 Form of Automatic Grant Option Agreement. ** 10.73 Supplementary Agreement, dated October 1, 1993, between the Company and Pfizer, Inc. to Agreement, dated May 1, 1991. ! 10.76 Amended Registration Rights Agreement, dated June 24, 1994, between the Company and the individuals listed on attached Schedule A, as amended (Exhibit 4.1). ! 10.77 First Addendum to Amended Registration Rights Agreement, dated July 6, 1994, between Company and Abbott Laboratories. (Exhibit 4.2). *** 10.78 Research, Development and License Agreement, dated July 6, 1994, between the Company and Abbott Laboratories (with certain confidential portions omitted). (Exhibit 10.75). *** 10.79 Stock and Note Purchase Agreement, dated September 2, 1994, between the Company and American Home Products Corporation (with certain confidential portions omitted). *** 10.80 Unsecured Convertible Promissory Note dated September 2, 1994, in the face amount of $10,000,000 executed by the Company in favor of American Home Products Corporation (with certain confidential portions omitted). (Exhibit 10.78). *** 10.81 Second Addendum to Amended Registration Rights Agreement, dated September 2, 1994, between the Company and American Home Products Corporation. *** 10.82 Research, Development and License 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). (Exhibit 10.77). *** 10.83 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). (Exhibit 10.80). *** 10.84 Distribution and Marketing Agreement, dated September 16, 1994, between the Company and Cetus Oncology Corporation, a wholly owned subsidiary of the Chiron Corporation (with certain confidential portions omitted). (Exhibit 10.82). & 10.93 Indemnity Agreement, dated June 3, 1995, between the Company, Allergan, Inc. and Allergan Ligand Retinoid Therapeutics, Inc. 4 EXHIBIT NO. DESCRIPTION -------- ----------- & 10.94 Tax Allocation Agreement, dated June 3, 1995, between the Company, Allergan, Inc. and Allergan Ligand Retinoid Therapeutics, Inc. & 10.95 Stock Purchase Agreement, dated June 3, 1995, between the Company, Allergan, Inc. and Allergan Pharmaceuticals (Ireland), Ltd. & 10.97 Research, Development and License Agreement, dated December 29, 1994, between SmithKline Beecham Corporation and the Company (with certain confidential portions omitted). & 10.98 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). & 10.99 Third Addendum to Amended Registration Rights Agreement, dated February 3, 1995, between S. R. One, Limited and the Company. # 10.100 PHOTOFRIN(R) Distribution Agreement, dated March 8, 1995, between the Company and Quadra Logic Technologies Inc. (with certain confidential portions omitted). 10.119(1) Option and Development Agreement, dated August 15, 1990, between Glycomed and Dr. Richard E. Galardy and Dr. Damian Grobelny with exhibit thereto (with certain portions omitted). (Exhibit 10 10.20). 10.120(1) Option and Development Agreement, dated November 27, 1989, between Glycomed and the President and Fellows of Harvard College with appendices thereto (with certain confidential portions omitted). (Exhibit 10.21) 10.121(1) Option and Development Agreement, dated January 1, 1991, between Glycomed and UAB Research Foundation with exhibits thereto (with certain confidential portions omitted). (Exhibit 10.22). 10.122(1) Joint Venture Agreement, dated December 18, 1990, among Glycomed, Glyko, Inc., Millipore Corporation, Astroscan, Ltd., Astromed, Ltd., Gwynn R. Williams and John Klock, M.D., with exhibits thereto (with certain confidential portions omitted). (Exhibit 10.23). 10.127(2) Research and License Agreement, dated April 29, 1992, between Glycomed and the Alberta Research Council with Appendix thereto (with certain confidential portions omitted). (Exhibit 10.28). 10.130(3) Amendment to Research and License Agreement, dated July 12, 1993, (confidential portions omitted). (Exhibit 10.32). 10.131(4) Amendments to Research and License Agreement, dated October 22, 1993, December 16, 19 and May 9, 1994 between Glycomed and the Alberta Research Council (with certain confidential portions omitted). (Exhibit 10.33). 10.132(4) License Agreement, dated February 14, 1994 between Glycomed and Sankyo Company, Ltd., for the Far East marketing rights of ophthalmic indications of Galardin(TM) MPI and analogs (with certain confidential portions omitted). (Exhibit 10.34). 10.133(4) Collaborative Technology Research and Development Agreement between Glycomed and Sankyo Company, Ltd., dated June 27, 1994 (with certain confidential portions omitted). (Exhibit 10.35). 10.136(5) Amendment to Research and License Agreement, dated September 22, 1994 between Glycomed and Alberta Research Council (with certain confidential portions omitted). (Exhibit 10.38). # 10.137 First Supplemental Indenture among the Company, Glycomed and Chemical Trust Company of California, Trustee. (Exhibit 10.133). %% 10.140 Promissory Notes, General Security Agreements and a Credit Terms and Conditions letter dated March 31, 1995, between the Company and Imperial Bank (Exhibit 10.101). - -- 10.142 Stock Purchase Agreement, dated June 27, 1995, between the Company and Sankyo Company, Ltd. - -- 10.143 Fifth Addendum to Amended Registration Rights Agreement, dated September 11, 1995 between the Company and Sankyo Company Limited. - -- 10.144 Stock Purchase Agreement, dated August 28, 1995, between the Company and Abbott Laboratories. - -- 10.145 Sixth Addendum to Amended Registration Rights Agreement, dated August 31, 1995, between the Company and Abbott Laboratories. - -- 10.146 Amendment to Research and Development Agreement, dated January 16, 1996, between the Company and American Home Products Corporation, as amended. 5 EXHIBIT NO. DESCRIPTION -------- ----------- - -- 10.147 Amendment to Stock Purchase Agreement, dated January 16, 1996, between the Company and American Home Products Corporation. - -- 10.148 Lease, dated July 6, 1994, between the Company and Chevron/Nexus partnership, First Amendment to lease dated July 6, 1994. X 10.149 Successor Employment Agreement, signed May 1, 1996, between the Company and David E. Robinson. x 10.150(6) Master Lease Agreement, signed May 30, 1996, between the Company and USL Capital Corporation. x 10.151 Settlement Agreement and Mutual Release of all Claims, signed April 20, 1996, between the Company and Pfizer, Inc. (with certain confidential portions omitted). x 10.152 Letter Amendment to Abbott Agreement, dated March 14, 1996, between the Company and Abbott Laboratories (with certain confidential portions omitted). Xx 10.153 Letter Agreement, dated August 8, 1996, between the Company and Dr. Andres Negro-Vilar. ## 10.154 Preferred Shares Rights Agreement, dated as of September 13, 1996, by and between Ligand Pharmaceuticals Incorporated and Wells Fargo Bank, N.A. (Exhibit 10.1). 10.155(6) Letter Agreement, dated November 4, 1996, between the Company and William Pettit. 10.156(6) Letter Agreement, dated February 6, 1997, between the Company and Russell L. Allen. 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. 10.159(6) Eighth Addendum to amended registration rights agreement, dated June 24, 1994, as amended between Ligand Pharmaceuticals and S.R. One, Limited and is effective as of February 10, 1997. 10.160(6) Seventh Addendum to amended registration rights agreement, dated June 24, 1994, as amended between Ligand Pharmaceuticals and S.R. One, Limited and is effective as of November 10, 1995. 10.161(7) Settlement Agreement, License and Mutual General Release between Ligand Pharmaceuticals and SRI/LJCRF, dated August 23, 1995 (with certain confidential portions omitted). 10.162(8) Limited Extension of Collaborative Technology Research, Option and Development Agreement between Ligand Pharmaceuticals and Sankyo Company Limited, dated June 24, 1997. 10.163(8) Extension of Master Lease Agreement between Lease Management Services and Ligand Pharmaceuticals dated July 29, 1997. 10.164(9) Third Amendment to Agreement, dated September 2, 1997, between the Company and American Home Products Corporation. 10.165(10) Amended and Restated Technology Cross License Agreement, dated September 24, 1997, among the Company, Allergan, Inc. and Allergan Ligand Retinoid Therapeutics, Inc. 10.166(10) Transition Agreement, dated September 24, 1997, among the Company, Allergan, Inc. and Allergan Ligand Retinoid Therapeutics, Inc. 10.167(10) Development and License Agreement, dated November 25, 1997, between the Company and Eli Lilly and Company (with certain confidential portions omitted). 10.168(10) 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(11) Option and Wholesale Purchase Agreement, dated November 25, 1997, between the Company and Eli Lilly and Company (with certain confidential portions omitted). 10.170(10) Stock Purchase Agreement, dated November 25, 1997, between the Company and Eli Lilly and Company. 10.171(10) First Amendment to Option and Wholesale Purchase Agreement dated February 23, 1998, between the Company and Eli Lilly and Company. 10.172(11) 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). 21.1(10) Subsidiaries of Registrant. 23.1(10) Consent of Ernst & Young LLP, Independent Auditors. 24.1(10) Power of Attorney. 27.1(10) Financial Data Schedule. 6 - ---------- * These exhibits were previously filed as part of, and are 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. % These exhibits were 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, 1992. ** These exhibits were 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. *** These exhibits were previously filed as part of, and are hereby incorporated by reference to, the same numbered exhibit (except as otherwise noted) filed with the Company's Quarterly Report on Form 10-Q for the period ended September 30, 1994. ! These exhibits were previously filed as part of, and are hereby incorporated by reference to, the exhibit filed with the Company's Form 8-K, filed on July 14, 1994. !! This exhibit was previously filed as part of, and is hereby incorporated by reference to Exhibit 99.1 filed with the Company's Form S-8 (No. 33-85366), filed on October 17, 1994. & These exhibits were previously filed as part of, and are 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. # These exhibits were previously filed as part of, and are hereby incorporated by reference to the numbered exhibit filed with the Registration Statement on Form S-4 (No. 33-90160) filed on March 9, 1995, as amended. %% 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. - -- These exhibits were filed previously, 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, 1995. x These exhibits were 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 June 30, 1996. Xx This exhibit was previously filed as part of, and are hereby incorporated by reference at the same numbered exhibit filed with the Company's Quarterly report on Form 10-Q for the period ended September 30, 1996. ## These exhibits were previously filed as part of, and are hereby incorporated by reference, the same numbered exhibit filed with the Company's Registration Statement on Form S-3 (No. 333-12603) filed on September 25, 1996, as amended. (1) Filed as an exhibit to Glycomed's Registration Statement on Form S-1 (No. 33-39961) filed on or amendments thereto and incorporated herein by reference. (2) Filed as an exhibit to Glycomed's Annual Report on Form 10-K (File No. 0-19161) filed on September 25, 1992 and incorporated herein by reference. (3) Filed as an exhibit to Glycomed's Annual Report on Form 10-K (File No. 0-19161) filed on September 13, 1993 and incorporated herein by reference. (4) Filed as an amendment to Glycomed's Annual Report on Form 10-K (File No. 0-19161) filed on September 27, 1994 and incorporated herein by reference. (5) Filed as an exhibit to Glycomed's Quarterly Report on Form 10-Q (File No. 0-19161) filed on February 10, 1995 and incorporated herein by reference. (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 Quarterly Report on Form 10-Q for the period ended March 31, 1997. (8) This exhibit was previously filed as part of, and is hereby incorporated by reference to the same same numbered exhibit filed with the Company's Quarterly Report on Form 10-Q for the period ended June 30, 1997. 7 (9) 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, 1997. (10) 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. (11) Refiled herewith after confidential treatment requested with respect to certain portions of this exhibit was denied by the Commission. Confidential treatment with respect to certain portions of this exhibit was granted. 8 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/ DAVID E. ROBINSON ------------------------------------------ David E. Robinson, President and Chief Executive Officer Date: November 24, 1998 Pursuant to the requirements of the Securities Exchange Act of 1934, 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/ DAVID E. ROBINSON Chairman of the Board, President, November 24, 1998 - ------------------------------------------------- Chief Executive Officer and Director David E. Robinson (Principal Executive Officer) /s/ PAUL V. MAIER Senior Vice President, Chief November 24, 1998 - ------------------------------------------------- Financial Officer and Treasurer Paul V. Maier (Principal Financial and Accounting Officer) - ------------------------------------------------- Director Henry F. Blissenbach * Director November 24, 1998 - ------------------------------------------------- Alexander D. Cross * Director November 24, 1998 - ------------------------------------------------- John Groom * Director November 24, 1998 - ------------------------------------------------- Irving S. Johnson * Director November 24, 1998 - ------------------------------------------------- Carl C. Peck * Director November 24, 1998 - ------------------------------------------------- Victoria R. Fash * By: /s/ DAVID E. ROBINSON ------------------------------------------- David E. Robinson Attorney-In-Fact