1

                                                                    EXHIBIT 99.1


                 AMENDMENT TO PREFERRED SHARES RIGHTS AGREEMENT

               THIS AMENDMENT (the "Amendment"), dated as of November 9, 1998,
is between Ligand Pharmaceuticals Incorporated, a Delaware corporation (the
"Company"), and ChaseMellon Shareholder Services, L.L.C., as Rights Agent (the
"Rights Agent").

                                    RECITALS

               A. The Company and the Rights Agent (as successor to Wells Fargo
Bank, N.A. which was acquired by the Rights Agent) are parties to a Preferred
Shares Rights Agreement dated as of September 13, 1996 (the "Rights Agreement").

               B. Elan Corporation, plc, a public limited company organized
under the laws of Ireland ("Elan"), Elan International Services, Ltd., a Bermuda
corporation and a wholly owned subsidiary of Elan ("EIS"), and the Company have
entered into a series of transactions (the "Elan Transactions"), pursuant to the
terms of that certain Stock Purchase Agreement, dated September 30, 1998 (the
"Stock Purchase Agreement"), by and between the Company and EIS, that certain
Securities Purchase Agreement, dated November 6, 1998 (the "Securities Purchase
Agreement"), by and between the Company, Elan and EIS, dated November 6, 1998,
and that certain Development, Licence and Supply Agreement, dated November 9,
1998 (the "License Agreement"), by and between the Company and Elan. The Stock
Purchase Agreement, the Securities Purchase Agreement and the License Agreement
are collectively referred to herein as the Elan Transaction Documents.

               C. The Board of Directors of the Company has approved the Elan
Transaction Documents and the Elan Transactions.

               D. Pursuant to Section 27 of the Rights Agreement, the Board of
Directors of the Company has determined that an amendment to the Rights
Agreement as set forth herein is necessary and desirable to reflect the
foregoing and certain other matters and the Company and the Rights Agent desire
to evidence such amendment in writing.

               Accordingly, the parties agree as follows:

               1. Amendment to definition of "Acquiring Person" set forth in
Section 1(a). The definition of "Acquiring Person" set forth in Section 1(a) of
the Rights Agreement is amended to add the following sentence at the end
thereof:

               "Notwithstanding anything in this Agreement to the contrary,
        neither Elan Corporation, plc, a public limited company organized under
        the laws of Ireland ("Elan"), nor Elan International Services, Ltd., a
        Bermuda corporation ("EIS"), nor any Affiliates of Elan or EIS shall be
        deemed to be an Acquiring Person by virtue of (i) their beneficial
        ownership on or before November 9, 2005 of an aggregate of up to
        twenty-five percent (25%) of the outstanding capital stock of


   2
the Company on a fully diluted basis or (ii) their beneficial ownership after
November 9, 2005 of a percentage of the then outstanding Common Shares, equal to
the percentage of the then outstanding Common Shares of the Company beneficially
owned by Elan, EIS and their Affiliates on November 9, 2005, to the extent their
beneficial ownership exceeds twenty percent (20%) on such date. In determining
whether Elan, EIS or any of their respective Affiliates shall be deemed to be an
Acquiring Person, shares of Common Stock that are beneficially owned by such
Person and acquired pursuant to the Securities Purchase Agreement, entered into
as of November 6, 1998, between the Company, Elan and EIS, as it may be amended
or supplemented from time to time (the "Securities Purchase Agreement"), and the
Development, Licence and Supply Agreement, entered into as of November 9, 1998,
between the Company and Elan, as it may be amended or supplemented from time to
time (the "License Agreement"), or upon conversion of the Company's Zero Coupon
Convertible Senior Notes due 2008 (the "Notes"), or which are beneficially owned
by such Person as a result of the ownership by such Person of the Notes, shall
not be counted unless such Person shall beneficially own additional shares of
Common Stock that are acquired by such Person other than pursuant to the Stock
Purchase Agreement entered into as of September 30, 1998, between the Company
and EIS, as it may be amended or supplemented from time to time (the "Stock
Purchase Agreement"), the Securities Purchase Agreement, the License Agreement
or the Notes.

               2. Amendment to definition of "Distribution Date" set forth in
Section 1(h). The definition of "Distribution Date" set forth in Section 1(h) of
the Rights Agreement is amended to add the following sentence at the end
thereof.

               "Notwithstanding anything in this Agreement to the contrary, a
        Distribution Date shall not be deemed to have occurred by virtue of (i)
        the beneficial ownership by Elan or EIS or any of their Affiliates on or
        before November 9, 2005, of an aggregate of up to twenty-five percent
        (25%) of the outstanding capital stock of the Company on a fully diluted
        basis pursuant to the terms of the Stock Purchase Agreement, the
        Securities Purchase Agreement and the License Agreement, or (ii) their
        beneficial ownership after November 9, 2005 of a percentage of the then
        outstanding Common Shares, equal to the percentage of the then
        outstanding Common Shares of the Company beneficially owned by Elan, EIS
        and their Affiliates on November 9, 2005, to the extent their beneficial
        ownership exceeds twenty percent (20%) on such date."

               3. Amendment to Section 2, "Appointment of Rights Agent." The
first sentence of Section 2 of the Rights Agreement is hereby modified and
amended by deleting "and the holders of the Rights (who in accordance with
Section 3 hereof, shall prior to the Distribution Date also be the holders of
the Common Shares)."

               4. Effectiveness. This Amendment shall be deemed effective as of
November 9, 1998, as if executed on such date. Except as amended hereby, the
Rights Agreement shall remain in full force and effect and shall be otherwise
unaffected hereby.

               5. Miscellaneous. This Amendment shall be deemed to be a contract
made under the laws of the State of Delaware and for all purposes shall be
governed by and construed in accordance with the laws of such State applicable
to contracts to be made and performed entirely within such State. This Amendment
may be executed in any number of counterparts, each of such counterparts shall
for all purposes be deemed to be an original, and all such counterparts shall
together constitute but one and the same instrument. If any term, provision,
covenant or restriction of this Amendment is held by a court of competent
jurisdiction or other authority to be invalid, void or unenforceable, the
remainder of the terms, provisions, covenants and restrictions of this Amendment
shall remain in full force and effect and shall in no way be affected, impaired
or invalidated.



   3

               EXECUTED as of the date first set forth above.


                                        LIGAND PHARMACEUTICALS
                                        INCORPORATED, a Delaware corporation


                                        /s/ DAVID E. ROBINSON
                                        ----------------------------------------
                                        David E. Robinson, President and Chief
                                        Executive Officer



                                        CHASEMELLON SHAREHOLDER SERVICES,
                                        L.L.C., as Successor Rights Agent


                                        /s/ ROSA M. BAUTISTA
                                        ----------------------------------------

                                        Name:  Rosa M. Bautista
                                               ---------------------------------
                                        Title: Relationship Manager
                                               ---------------------------------





                         [SIGNATURE PAGE TO AMENDMENT TO
                       PREFERRED SHARES RIGHTS AGREEMENT]