Exhibit 10.1

SECOND AMENDMENT

TO

LOAN AND SECURITY AGREEMENT

This Second Amendment to Loan and Security Agreement (the “Amendment”), is
entered into as of March 29, 2012, by and between SQUARE 1 BANK (the “Bank”) and
LIGAND PHARMACEUTICALS INCORPORATED (the “Borrower”).

RECITALS

Borrower and Bank are parties to that certain Loan and Security Agreement dated
as of March 31, 2011 (as amended from time to time, the “Agreement”). The
parties desire to amend the Agreement in accordance with the terms of this
Amendment.

NOW, THEREFORE, the parties agree as follows:

 

1) Section 6.3 of the Agreement is hereby amended and restated, in its entirety,
as follows:

6.3 Cash Security Account. Borrower shall at all times maintain the Cash
Security Account, with a balance of Cash in such Cash Security Account at all
times of not less than the total amount outstanding under the Revolving Line.

 

2) The following definitions in Exhibit A to the Agreement are hereby amended
and restated, in their entirety, as follows:

“Cash Security Account” means segregated money market account no. 7002291, held
at Bank as collateral for Borrower’s Obligations, in an amount equal to or
greater than the total amount outstanding under the Revolving Line.

“Collateral” means Cash held in the Cash Security Account and pledged to Bank as
security for the Obligations, which shall at all times be in an amount equal to
or greater than the total amount outstanding under the Revolving Line.

“Revolving Maturity Date” means March 28, 2013.

 

3) Unless otherwise defined, all initially capitalized terms in this Amendment
shall be as defined in the Agreement. The Agreement, as amended hereby, shall be
and remain in full force and effect in accordance with its respective terms and
hereby is ratified and confirmed in all respects. Except as expressly set forth
herein, the execution, delivery, and performance of this Amendment shall not
operate as a waiver of, or as an amendment of, any right, power, or remedy of
Bank under the Agreement, as in effect prior to the date hereof. Borrower
ratifies and reaffirms the continuing effectiveness of all agreements entered
into in connection with the Agreement.

 

4) Borrower represents and warrants that the representations and warranties
contained in the Agreement are true and correct as of the date of this
Amendment.

 

Ligand Pharmaceuticals Incorporated – 2nd Amendment to LSA

 

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5) This Amendment may be executed in two or more counterparts, each of which
shall be deemed an original, but all of which together shall constitute one
instrument.

 

6) As a condition to the effectiveness of this Amendment, Bank shall have
received, in form and substance satisfactory to Bank, the following:

 

  a) this Amendment, duly executed by Borrower;

 

  b) an officer’s certificate of Borrower with respect to incumbency and
resolutions authorizing the execution of this Amendment;

 

  c) payment of all Bank Expenses, including Bank’s expenses for the
documentation of this Amendment and any related documents, and any UCC, good
standing and intellectual property search or filing fees, which may be debited
from any of Borrower’s accounts; and

 

  d) such other documents and completion of such other matters, as Bank may
reasonably deem necessary or appropriate.

[Signature Page Follows]

 

Ligand Pharmaceuticals Incorporated – 2nd Amendment to LSA

 

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IN WITNESS WHEREOF, the undersigned have executed this Amendment as of the first
date above written.

 

LIGAND PHARMACEUTICALS INCORPORATED     SQUARE 1 BANK By:  

        /s/ John Sharp

    By:  

        /s/ Patrick Cahill

Name:           John Sharp     Name:           Patrick Cahill Title:  
        CFO     Title:           AVP

[Signature Page to Second Amendment to Loan and Security Agreement]

 

Ligand Pharmaceuticals Incorporated – 2nd Amendment to LSA

 

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