PCOP Pharmacopeia (MM)

As Filed with the Securities and Exchange Commission on December 23, 2008

Registration No. 333-145393

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

POST-EFFECTIVE AMENDMENT NO. 1
TO

FORM S-3

REGISTRATION STATEMENT
UNDER
THE SECURITIES ACT OF 1933

PHARMACOPEIA, INC.

(Exact name of registrant as specified in its charter)

P.O. Box 5350

Princeton, New Jersey 08543-5350

(609) 452-3600
(Address, including zip code, and telephone number, including area code, of registrant’s principal executive
offices)

Stephen C. Costalas, Esq.
Executive Vice President, Corporate Development, General Counsel and Secretary
Pharmacopeia, Inc.
P.O. Box 5350
Princeton, New Jersey 08543-5350
(609) 452-3600

(Name, address including zip code, and telephone number, including
area code, of agent for service)

With a copy to:
Ella DeTrizio, Esq.
Dechert LLP
Suite 500, 902 Carnegie Center
Princeton, New Jersey 08540-6531
(609) 955-3211

If the only securities being registered on this Form are being offered pursuant to dividend or interest reinvestment plans, please check the following box: o

If any of the securities being registered on this Form are to be offered on a delayed or continuous basis pursuant to Rule 415 under the Securities Act of 1933, other than securities offered only in connection with dividend or interest reinvestment plans, check the following box: o

If this Form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, please check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. o

If this Form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. o

If this Form is a registration statement pursuant to General Instruction I.D. or a post-effective amendment thereto that shall become effective upon filing with the Commission pursuant to Rule 462(e) under the Securities Act, check the following box. o

If this Form is a post-effective amendment to a registration statement filed pursuant to General Instruction I.D. filed to register additional securities or additional classes of securities pursuant to Rule 413(b) under the Securities Act, check the following box. o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

DEREGISTRATION OF SECURITIES

Pharmacopeia, Inc. (the “ Registrant ”) is filing this Post-Effective Amendment No. 1 to its Registration Statement on Form S-3 to withdraw and remove from registration any and all unissued and unsold shares of the Registrant’s common stock, par value $0.01 per share; shares of the Registrant’s preferred stock, $0.01 par value per share; debt securities; warrants; and units (collectively, the “ Unsold Securities ”), issuable by the Registrant pursuant to its Registration Statement on Form S-3 filed with the Securities and Exchange Commission on August 13, 2007 (Registration No. 333-145393) (the “ Registration Statement ”).

On December 23, 2008, the Registrant’s stockholders approved, at a special meeting of stockholders, an Agreement and Plan of Merger, dated as of September 24, 2008 (the “ Merger Agreement ”), by and among the Registrant, Ligand Pharmaceuticals Incorporated, a Delaware corporation (“ Ligand ”), Margaux Acquisition Corp., a Delaware corporation and wholly-owned subsidiary of Ligand (“ Margaux ”), and Latour Acquisition, LLC, a Delaware corporation and wholly-owned subsidiary of Ligand (“ Latour ”), and the transactions contemplated by the Merger Agreement. Pursuant to the Merger Agreement, on December 23, 2008, Margaux was merged with and into the Registrant (“ Merger 1 ”), immediately followed by the merger of the Registrant, the surviving corporation of Merger 1, with and into Latour (“ Merger 2 ”), with Latour continuing after Merger 2 as the surviving entity.

At the effective time of Merger 1, each share of the Registrant’s common stock, par value $0.01 per share, issued and outstanding immediately prior to Merger 1 (other than shares with respect to which appraisal rights were properly exercised under Delaware law) was cancelled and converted into the right to receive (i) 0.5985 shares of common stock, par value $0.001 per share, of Ligand, and (ii) $0.31 in cash, without interest and less any required withholding taxes. These values exclude a potential for approximately $0.50 per share related to contingent value rights (“ CVRs ”) received by each holder of the Registrant’s common stock at the effective time of Merger 1. The CVRs provide each such stockholder the right to receive a proportionate share of an aggregate of $15 million if Ligand enters into a license, sale, development, marketing or option agreement with respect to any product candidate from the Registrant’s dual angiotensin and endothelin receptor antagonist program, of which the lead clinical product candidate is PS433540 (other than any agreement with Bristol-Myers Squibb Company or any of its affiliates), on or prior to December 31, 2011.

As a result of Merger 1, the Registrant terminated all offerings of its securities pursuant to its existing registration statements, including the Registration Statement. In accordance with an undertaking made by the Registrant in the Registration Statement to remove from registration, by means of a post-effective amendment, any Unsold Securities which remain unsold at the termination of the offering, the Registrant hereby removes from registration all Unsold Securities registered but unsold under the Registration Statement.

2

SIGNATURES

Pursuant to the requirements of the Securities Act of 1933, as amended, the Registrant certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-3 and has duly caused this Post-Effective Amendment No. 1 to the Registration Statement to be signed on its behalf by the undersigned, thereunto duly authorized, in the Township of Cranbury, State of New Jersey, on this 23rd day of December, 2008.

Pursuant to the requirements of the Securities Act of 1933, this Post-Effective Amendment No. 1 to the Registration Statement on Form S-3 has been signed by the following persons in the capacities and on the dates indicated.

3