EXHIBIT 10.1
                               SECOND AMENDMENT TO
                           THE LIGAND PHARMACEUTICALS
                     NONQUALIFIED DEFERRED COMPENSATION PLAN

        THIS SECOND AMENDMENT TO THE LIGAND PHARMACEUTICALS NONQUALIFIED
DEFERRED COMPENSATION PLAN (this "Amendment"), effective as of December 8, 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, as amended (the "Plan").

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

         WHEREAS, the Board of Directors of the Company 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. Section 6.7 of the Plan is hereby amended to read as follows:

                  6.7 Termination Distributions. Notwithstanding anything to the
         contrary contained in the Plan or the Trust, each Participant in the
         Plan who is not currently receiving distributions on December 8, 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 Election 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 23, 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.


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