EXHIBIT 10.1

                               FIRST AMENDMENT TO
                           THE LIGAND PHARMACEUTICALS
                     NONQUALIFIED DEFERRED COMPENSATION PLAN

        THIS FIRST AMENDMENT TO THE LIGAND PHARMACEUTICALS NONQUALIFIED DEFERRED
COMPENSATION PLAN (this "AMENDMENT"), effective as of July 5, 2005, is made and
adopted by LIGAND PHARMACEUTICALS INCORPORATED, a Delaware corporation (the
"COMPANY"). Capitalized terms used but not otherwise defined herein shall have
the meanings ascribed to them in the Plan (as defined below).

                                    RECITALS

         WHEREAS, the Company maintains the Ligand Pharmaceuticals Nonqualified
Deferred Compensation Plan (the "PLAN").

         WHEREAS, pursuant to Section 11.10 of the Plan, the Plan may be amended
by the Company.

         WHEREAS, the Company, by action of the Compensation Committee of the
Board of Directors, desires to amend the Plan as set forth below.

         NOW, THEREFORE, in consideration of the foregoing, the Company hereby
amends the Plan as follows:

         1. A new Section 6.7 is hereby added to the Plan as follows:

                  6.7 TERMINATION DISTRIBUTIONS. Notwithstanding anything to the
         contrary contained in the Plan or the Trust, each Participant serving
         as the Employer's Chief Executive Officer or Executive Vice President
         on July 5, 2005 (each, an "ELIGIBLE PARTICIPANT") may make a one-time
         election to terminate his or her participation in the Plan, cancel his
         or her existing Deferral Elections and to receive a distribution of all
         amounts credited to his or her Account(s) during 2005 (an "EARLY
         TERMINATION ELECTION"). An Early Termination Elections must be made
         with respect to all amounts credited to an Eligible Participant's
         Account(s); partial Early Termination Elections will not be permitted.
         An Eligible Participant must deliver a written Early Termination
         Election to the Administrator no later than December 1, 2005. All
         amounts credited to an Eligible Participant's Account(s) will be
         distributed in a lump sum as soon as administratively feasible
         following the Administrator's receipt of the Eligible Participant's
         Early Termination Election, but in no event later than December 31,
         2005 (an "EARLY TERMINATION DISTRIBUTION"). An Eligible Participant who
         makes an Early Termination Election under this section shall cease his
         or her participation in the Plan and all of such Eligible Participant's
         existing Deferral Elections shall be cancelled as of the date such
         Eligible Participant receives his or her Early Termination
         Distribution. An Eligible Participant who makes an Early Termination
         Election under this section shall not be permitted to make Deferrals
         with respect to any Compensation payable to such Eligible Participant
         during the remainder of the Plan Year ending December 31, 2005 and
         shall not receive any Employer Contributions under the Plan for the
         remainder of the Plan Year ending December 31, 2005.

         2. All other terms and provisions of the Plan shall remain unchanged
         except as specifically modified herein. The Plan, as amended by this
         Amendment, is hereby ratified and confirmed.