Second Amendment to Loan and Security Agreement



 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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