Secured Promissory Note ($3,500,000 principal amount)



 Exhibit 10.3 
 SECURED PROMISSORY NOTE 
  

			
	$3,500,000	  	January 23, 2012

 FOR VALUE RECEIVED, LIGAND PHARMACEUTICALS INCORPORATED, a Delaware corporation, and each of the other
Persons signing below as a Borrower (individually, a “Borrower” and, collectively, the “Borrowers”) jointly and severally PROMISE TO PAY to the order of OXFORD FINANCE LLC (“Lender”) the
principal amount of THREE MILLION FIVE HUNDRED THOUSAND DOLLARS ($3,500,000) or such lesser amount as shall equal the outstanding principal balance of the Term B Loan made to Borrowers by Lender, plus interest on the aggregate unpaid principal
amount of Term B Loan, at the rates and in accordance with the terms of the Loan and Security Agreement dated as of January 24, 2011 by and among Borrowers, Oxford Finance LLC, as Collateral Agent and as a Lender, and Lenders from time to time
party thereto (as amended, restated, supplemented or otherwise modified from time to time, the “Loan Agreement”). If not sooner paid, the entire principal amount and all accrued and unpaid interest hereunder shall be due and payable
on the Maturity Date as set forth in the Loan Agreement. Any capitalized term not otherwise defined herein shall have the meaning attributed to such term in the Loan Agreement. 
 Borrowers agree to pay any initial partial monthly interest payment from the date the Term B Loan is made to Borrowers under this Secured Promissory Note (this “Note”) to the first
Payment Date (“Interim Interest”) on the first Payment Date. 
 Principal, interest and all other amounts due with respect to
the Term B Loan, are payable in lawful money of the United States of America to Lender as set forth in the Loan Agreement and this Note. The principal amount of this Note and the interest rate applicable thereto, and all payments made with respect
thereto, shall be recorded by Lender and, prior to any transfer hereof, endorsed on the grid attached hereto which is part of this Note. 
 The
Loan Agreement, among other things, (a) provides for the making of a secured Term Loan by Lender to Borrowers, and (b) contains provisions for acceleration of the maturity hereof upon the happening of certain stated events. 

This Note may not be prepaid except as set forth in Section 2.2 (c) and Section 2.2(d) of the Loan Agreement. 

This Note and the obligation of Borrowers to repay the unpaid principal amount of the Term B Loan, interest on the Term B Loan and all other amounts due
Lender under the Loan Agreement is secured under the Loan Agreement. 
 Presentment for payment, demand, notice of protest and all other demands
and notices of any kind in connection with the execution, delivery, performance and enforcement of this Note are hereby waived. 
 Borrowers
shall pay all reasonable fees and expenses, including, without limitation, reasonable attorneys’ fees and costs, incurred by Lender in the enforcement or attempt to enforce any of a Borrower’s obligations hereunder not performed when due.

 This Note shall be governed by, and construed and interpreted in accordance with, the internal laws of the State of California. 

The ownership of an interest in this Note shall be registered on a record of ownership maintained by Lender or its agent. Notwithstanding anything else
in this Note to the contrary, the right to the principal of, and stated interest on, this Note may be transferred only if the transfer is registered on such record of ownership and the transferee is identified as the owner of an interest in the
obligation. Borrowers shall be entitled to treat the registered holder of this Note (as recorded on such record of ownership) as the owner in fact thereof for all purposes and shall not be bound to recognize any equitable or other claim to or
interest in this Note on the part of any other person or entity. Unless and until Lender notifies Borrowers in writing that such a registered transfer has occurred and that it is so recorded on the record of ownership, Borrowers shall be entitled to
act as if there has been no such transfer and no such recordation on the record of ownership. 







 IN WITNESS WHEREOF, Borrowers have caused this Note to be duly executed by one of its
officers thereunto duly authorized on the date hereof. 
  

									
	LIGAND PHARMACEUTICALS INCORPORATED	 		 	CYDEX PHARMACEUTICALS, INC.
					
	 By
	 	/s/     John P. Sharp	 		 	By	 	/s/     John P. Sharp
	 Name:
 Title:
	 	 John P. Sharp

Vice President, Finance and Chief Financial Officer
	 		 	 Name:
 Title:
	 	 John P. Sharp
 Vice
President and Chief Financial Officer

				
	SERAGEN, INC.	 		 		 	
					
	 By
	 	/s/     John P. Sharp	 		 		 	
	 Name:
 Title:
	 	 John P. Sharp
 Vice President
and Chief Financial Officer
	 		 		 	
				
	METABASIS THERAPEUTICS, INC.	 		 		 	
					
	 By
	 	/s/     John P. Sharp	 		 		 	
	 Name:
 Title:
	 	 John P. Sharp
 Vice President
and Chief Financial Officer
	 		 		 	
				
	PHARMACOPEIA, LLC	 		 		 	
				
	 By: Ligand Pharmaceuticals Incorporated,
 Its Sole and Managing Member
	 		 		 	
					
	         By
	 	/s/     John P. Sharp	 		 		 	
	         Name:

        Title:
	 	 John P. Sharp
 Vice President,
Finance and Chief Financial Officer
	 		 		 	
				
	NEUROGEN CORPORATION	 		 		 	
					
	 By
	 	/s/     John P. Sharp	 		 		 	
	 Name:
 Title:
	 	 John P. Sharp
 Vice President
and Chief Financial Officer
	 		 		 	
				
	ALLERGAN LIGAND RETINOID THERAPEUTICS, INC.	 		 		 	
					
	 By
	 	/s/     John P. Sharp	 		 		 	
	 Name:
 Title:
	 	 John P. Sharp
 Chief Financial
Officer
	 		 		 	
				
	LIGAND JVR, INC.	 		 		 	
					
	 By
	 	/s/     John P. Sharp	 		 		 	
	 Name:
 Title:
	 	 John P. Sharp
 Chief Financial
Officer
	 		 		 	








 LOAN INTEREST RATE AND PAYMENTS OF PRINCIPAL 

 

									
	 Date
	 	 Principal

Amount
	 	 Interest Rate
	  	Scheduled
Payment Amount	  	Notation By








 Amortization Table 

(Term B Loan; Note 2) 
 Attached. 







 Oxford Finance LLC 

Amortization Table 
 Ligand AA02b 
  

													
	 	Start Date:	  	  	 	1/23/2012	  	 				 	Disclaimer:
	 	Interest Rate:	  	  	 	8.9012 	% 	 				 	THIS IS A STANDARD AMORTIZATION
	 	Term:	  	  	 	30	  	 	 	12IO + 18PI	  	 	SCHEDULE. IT IS NOT INTENDED TO BE
	 	Payment:	  	  	$	208,433.35	  	 				 	USED FOR PAYOFF PURPOSES.
	 	Final Payment:	  	  	$	210,000.00	  	 	 	6.00	% 	 	
	 	Amount:	  	  	 	3,500,000.00	  	 				 	

  

																									
	 PMT
No.
	  	Payment
Date	 	  	Beginning
Balance	 	  	Monthly
Payment	 	  	Interest	 	  	Principal	 	  	Ending
Balance	 
		  	 	2/1/12	  	  	 	Interim Interest Due -Billed Seperately	  	  	$	3,500,000.00	  
	 1
	  	 	3/1/12	  	  	$	3,500,000.00	  	  	$	25,961.83	  	  	$	25,961.83	  	  	$	0.00	  	  	$	3,500,000.00	  
	 2
	  	 	4/1/12	  	  	$	3,500,000.00	  	  	$	25,961.83	  	  	$	25,961.83	  	  	$	0.00	  	  	$	3,500,000.00	  
	 3
	  	 	5/1/12	  	  	$	3,500,000.00	  	  	$	25,961.83	  	  	$	25,961.83	  	  	$	0.00	  	  	$	3,500,000.00	  
	 4
	  	 	6/1/12	  	  	$	3,500,000.00	  	  	$	25,961.83	  	  	$	25,961.83	  	  	$	0.00	  	  	$	3,500,000.00	  
	 5
	  	 	7/1/12	  	  	$	3,500,000.00	  	  	$	25,961.83	  	  	$	25,961.83	  	  	$	0.00	  	  	$	3,500,000.00	  
	 6
	  	 	8/1/12	  	  	$	3,500,000.00	  	  	$	25,961.83	  	  	$	25,961.83	  	  	$	0.00	  	  	$	3,500,000.00	  
	 7
	  	 	9/1/12	  	  	$	3,500,000.00	  	  	$	25,961.83	  	  	$	25,961.83	  	  	$	0.00	  	  	$	3,500,000.00	  
	 8
	  	 	10/1/12	  	  	$	3,500,000.00	  	  	$	25,961.83	  	  	$	25,961.83	  	  	$	0.00	  	  	$	3,500,000.00	  
	 9
	  	 	11/1/12	  	  	$	3,500,000.00	  	  	$	25,961.83	  	  	$	25,961.83	  	  	$	0.00	  	  	$	3,500,000.00	  
	 10
	  	 	12/1/12	  	  	$	3,500,000.00	  	  	$	25,961.83	  	  	$	25,961.83	  	  	$	0.00	  	  	$	3,500,000.00	  
	 11
	  	 	1/1/13	  	  	$	3,500,000.00	  	  	$	25,961.83	  	  	$	25,961.83	  	  	$	0.00	  	  	$	3,500,000.00	  
	 12
	  	 	2/1/13	  	  	$	3,500,000.00	  	  	$	25,961.83	  	  	$	25,961.83	  	  	$	0.00	  	  	$	3,500,000.00	  
	 13
	  	 	3/1/13	  	  	$	3,500,000.00	  	  	$	208,433.35	  	  	$	25,961.83	  	  	$	182,471.51	  	  	$	3,317,528.49	  
	 14
	  	 	4/1/13	  	  	$	3,317,528.49	  	  	$	208,433.35	  	  	$	24,608.32	  	  	$	183,825.03	  	  	$	3,133,703.46	  
	 15
	  	 	5/1/13	  	  	$	3,133,703.46	  	  	$	208,433.35	  	  	$	23,244.77	  	  	$	185,188.58	  	  	$	2,948,514.88	  
	 16
	  	 	6/1/13	  	  	$	2,948,514.88	  	  	$	208,433.35	  	  	$	21,871.10	  	  	$	186,562.25	  	  	$	2,761,952.63	  
	 17
	  	 	7/1/13	  	  	$	2,761,952.63	  	  	$	208,433.35	  	  	$	20,487.24	  	  	$	187,946.10	  	  	$	2,574,006.52	  
	 18
	  	 	8/1/13	  	  	$	2,574,006.52	  	  	$	208,433.35	  	  	$	19,093.12	  	  	$	189,340.23	  	  	$	2,384,666.30	  
	 19
	  	 	9/1/13	  	  	$	2,384,666.30	  	  	$	208,433.35	  	  	$	17,688.66	  	  	$	190,744.69	  	  	$	2,193,921.61	  
	 20
	  	 	10/1/13	  	  	$	2,193,921.61	  	  	$	208,433.35	  	  	$	16,273.78	  	  	$	192,159.57	  	  	$	2,001,762.04	  
	 21
	  	 	11/1/13	  	  	$	2,001,762.04	  	  	$	208,433.35	  	  	$	14,848.40	  	  	$	193,584.94	  	  	$	1,808,177.10	  
	 22
	  	 	12/1/13	  	  	$	1,808,177.10	  	  	$	208,433.35	  	  	$	13,412.45	  	  	$	195,020.89	  	  	$	1,613,156.20	  
	 23
	  	 	1/1/14	  	  	$	1,613,156.20	  	  	$	208,433.35	  	  	$	11,965.85	  	  	$	196,467.49	  	  	$	1,416,688.71	  
	 24
	  	 	2/1/14	  	  	$	1,416,688.71	  	  	$	208,433.35	  	  	$	10,508.52	  	  	$	197,924.82	  	  	$	1,218,763.89	  
	 25
	  	 	3/1/14	  	  	$	1,218,763.89	  	  	$	208,433.35	  	  	$	9,040.38	  	  	$	199,392.96	  	  	$	1,019,370.92	  
	 26
	  	 	4/1/14	  	  	$	1,019,370.92	  	  	$	208,433.35	  	  	$	7,561.35	  	  	$	200,871.99	  	  	$	818,498.93	  
	 27
	  	 	5/1/14	  	  	$	818,498.93	  	  	$	208,433.35	  	  	$	6,071.35	  	  	$	202,362.00	  	  	$	616,136.93	  
	 28
	  	 	6/1/14	  	  	$	616,136.93	  	  	$	208,433.35	  	  	$	4,570.30	  	  	$	203,863.05	  	  	$	412,273.88	  
	 29
	  	 	7/1/14	  	  	$	412,273.88	  	  	$	208,433.35	  	  	$	3,058.11	  	  	$	205,375.24	  	  	$	206,898.64	  
	 30
	  	 	8/1/14	  	  	$	206,898.64	  	  	$	208,433.35	  	  	$	1,534.71	  	  	$	206,898.64	  	  	$	0.00	  
		  	 	8/1/14	  	  	 	Final Payment	  	  	$	210,000.00	  	  	$	210,000.00	  	  	$	0.00	  	  			
		  				  				  	  
	  
	 	  	  
	  
	 	  	  
	  
	 	  			
		  				  	 	Totals	  	  	$	4,273,342.27	  	  	$	773,342.27	  	  	$	3,500,000.00