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Exhibit 4.1  



	

 	
 	
PHARMACOPEIA DRUG DISCOVERY, INC.	
 	

 
	NUMBER	 	 	 	 	 	 	 	SHARES
	PD	 	 	 	 	 	 	 	 
	 	 	INCORPORATED UNDER THE LAWS OF THE STATE OF DELAWARE	 	 	 	SEE REVERSE FOR CERTAIN DEFINITIONS	 	 
	 	 	 	 	 	 	CUSIP 7171EP 10 1	 	 
	

 	
 	
This Certifies that            	
 	

 	
 	

 	
 	

 
	

    	
 	

 	
 	

 	
 	

 	
 	

 
	

 	
 	

is the registered holder of            	
 	

 	
 	

 
	

 	
 	
FULLY-PAID AND NON-ASSESSABLE SHARES OF THE COMMON STOCK, PAR VALUE $.01, OF	
 	

 
	

 	
 	
PHARMACOPEIA DRUG DISCOVERY, INC.	
 	

 
	(hereinafter called the Corporation), transferable on the books of the Corporation by the holder hereof in person or by duly authorized attorney, upon surrender of this certificate properly endorsed. This certificate and
the shares represented hereby are issued and shall be held subject to all the provisions of the Certificate of Incorporation of the Corporation, as amended and restated, and the Bylaws of the Corporation, as amended and restated, to all of which the
holder of this certificate, by acceptance hereof, assents. This certificate is not valid until countersigned and registered by the Transfer Agent and Registrar.
	

 	
 	
WITNESS the facsimile seal of the Corporation and the facsimile signature of its duly authorized officers.	
 	

 
	

 	
 	

Dated:             	
 	

 	
 	

 	
 	

 
	

 	
 	

 	
 	

COUNTERSIGNED AND REGISTERED:	
 	

 
	 	 	 	 	AMERICAN STOCK TRANSFER & TRUST COMPANY
	 	 	 	 	 	 	TRANSFER AGENT AND REGISTRAR	 	 
	 	 	 	 	BY	 	 	 	 
	

 	
 	

 	
 	

 	
 	

AUTHORIZED SIGNATURE	
 	

 
	

 	
 	

/s/ Brian M. Pooner	
 	

[SEAL]	
 	

/s/ Joseph A. Mollica	
 	

 
	 	 	SECRETARY	 	 	 	CHAIRMAN, PRESIDENT AND CHIEF EXECUTIVE OFFICER

	 	 







  
 

    PHARMACOPEIA DRUG DISCOVERY, INC.    
    


        THE CORPORATION IS AUTHORIZED TO ISSUE SHARES OF PREFERRED STOCK AND THE BOARD OF DIRECTORS OF THE CORPORATION IS AUTHORIZED TO DETERMINE THE DESIGNATIONS,
RELATIVE RIGHTS, PREFERENCES AND LIMITATIONS APPLICABLE TO DIFFERENT CLASSES OF PREFERRED STOCK AND DIFFERENT SERIES WITHIN A CLASS OF PREFERRED STOCK. THE CORPORATION WILL FURNISH WITHOUT CHARGE TO
EACH STOCKHOLDER WHO SO REQUESTS THE POWERS, DESIGNATIONS, PREFERENCES AND RELATIVE, PARTICIPATING, OPTIONAL OR OTHER SPECIAL RIGHTS OF EACH CLASS OF STOCK OR SERIES
THEREOF WHICH THE CORPORATION IS AUTHORIZED TO ISSUE AND THE QUALIFICATIONS, LIMITATIONS OR RESTRICTIONS OF SUCH PREFERENCES AND/OR RIGHTS. ANY SUCH REQUEST SHOULD BE MADE TO THE CORPORATION OR TO THE
TRANSFER AGENT. 


        The
following abbreviations, when used in the inscription on the face of this certificate, shall be construed as though they were written out in full according to applicable laws or
regulations: 



	TEN COM	—	 	as tenants in common	 	 	 	UNIF GIFT MIN ACT	—	 	
	 	Custodian	 	

	TEN ENT	—	 	as tenants by the entireties	 	 	 	 	 	 	(Cust)	 	 	 	(Minor)
	JT TEN	—	 	as joint tenants with right of survivorship and not as tenants in common	 	 	 	 	 	 	under Uniform Gifts to Minors Act

    
 (State)
	 	 	 	 	 	 	 	UNIF TRF MIN ACT	—	 	
	 	Custodian (until age       )	 	

	 	 	 	 	 	 	 	 	 	 	(Cust)	 	 	 	(Minor)
	 	 	 	 	 	 	 	 	 	 	under Uniform Transfers to Minors Act

    
 (State)




Additional abbreviations may also be used though not in the above list 


        FOR VALUE RECEIVED,
                                         
                                          
                                          
                    hereby sell, assign and transfer unto
 



	PLEASE INSERT SOCIAL SECURITY OR OTHER IDENTIFYING NUMBER OF ASSIGNEE


    
	 	 	 	 	 
	

    
(PLEASE PRINT OR TYPEWRITE NAME AND ADDRESS, INCLUDING ZIP CODE, OF ASSIGNEE)
	    

	    

	    
	Shares
	of the common stock represented by the within Certificate, and do hereby irrevocably constitute and appoint
	    
	Attorney
	to transfer the said stock on the books of the within named Corporation with full power of substitution in the premises.





	

Dated	
 	

    
	
 	

 
	 	 	X	 	    

	 	 	X	 	    

	 	 	NOTICE:	 	THE SIGNATURE(S) TO THIS ASSIGNMENT MUST CORRESPOND WITH THE NAME(S) AS WRITTEN UPON THE FACE OF THE CERTIFICATE IN EVERY PARTICULAR, WITHOUT ALTERATION OR ENLARGEMENT OR ANY CHANGE WHATSOEVER.
	Signature(s) Guaranteed	 	 





	By	 	    
 THE SIGNATURE(S) SHOULD BE GUARANTEED BY AN ELIGIBLE GUARANTOR INSTITUTION (BANKS, STOCKBROKERS, SAVINGS AND LOAN ASSOCIATIONS AND CREDIT UNIONS WITH MEMBERSHIP IN
AN APPROVED SIGNATURE GUARANTEE MEDALLION PROGRAM), PURSUANT TO S.E.C. RULE 17Ad-15.	 	 
	    	 	 	 	 











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