<SUBMISSION>
<ACCESSION-NUMBER>0001047469-04-012631
<TYPE>8-K
<PUBLIC-DOCUMENT-COUNT>2
<PERIOD>20040419
<ITEMS>5
<ITEMS>7
<FILING-DATE>20040420
<FILER>
<COMPANY-DATA>
<CONFORMED-NAME>PHARMACOPEIA INC
<CIK>0001002388
<ASSIGNED-SIC>7372
<IRS-NUMBER>330557266
<STATE-OF-INCORPORATION>DE
<FISCAL-YEAR-END>1231
</COMPANY-DATA>
<FILING-VALUES>
<FORM-TYPE>8-K
<ACT>34
<FILE-NUMBER>000-27188
<FILM-NUMBER>04742344
</FILING-VALUES>
<BUSINESS-ADDRESS>
<STREET1>CN 5350
<CITY>PRINCETON
<STATE>NJ
<ZIP>08543-5350
<PHONE>6094523600
</BUSINESS-ADDRESS>
<MAIL-ADDRESS>
<STREET1>CN 5350
<CITY>PRINCETON
<STATE>NJ
<ZIP>08543-5350
</MAIL-ADDRESS>
</FILER>
<DOCUMENT>
<TYPE>8-K
<SEQUENCE>1
<FILENAME>a2134150z8-k.htm
<DESCRIPTION>8-K
<TEXT>
<HTML>
<HEAD>

</HEAD>
<BODY BGCOLOR="#FFFFFF" LINK=BLUE  VLINK=PURPLE>
<BR>
<FONT SIZE=3 ><A HREF="#04SAN1173_1">QuickLinks</A></FONT>
<font size=3> -- Click here to rapidly navigate through this document</font>

<P><FONT SIZE=2>
<hr noshade width=100% align=left size=4>
<hr noshade width=100% align=left size=1> </FONT></P>

<P ALIGN="CENTER"><FONT SIZE=5><B>UNITED STATES<BR>
SECURITIES AND EXCHANGE COMMISSION<BR>  </B></FONT><FONT SIZE=2><B>Washington, D.C. 20549  </B></FONT></P>

<P ALIGN="CENTER"><FONT SIZE=5><B>FORM 8-K  </B></FONT></P>

<P ALIGN="CENTER"><FONT SIZE=3><B>CURRENT REPORT  </B></FONT></P>

<P ALIGN="CENTER"><FONT SIZE=3><B> Pursuant to Section&nbsp;13 or 15(d) of the Securities Exchange Act of 1934  </B></FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2>Date of Report (Date of earliest event reported): April&nbsp;19, 2004 </FONT></P>

<P ALIGN="CENTER"><FONT SIZE=5><B>PHARMACOPEIA,&nbsp;INC.<BR>  </B></FONT><FONT SIZE=2>(Exact name of registrant as specified in its charter) </FONT></P>

<!-- User-specified TAGGED TABLE -->
<TABLE WIDTH="100%" BORDER=0 CELLSPACING=0 CELLPADDING=0>
<TR VALIGN="TOP">
<TD WIDTH="32%" ALIGN="CENTER"><FONT SIZE=2><B>Delaware<BR> </B></FONT><FONT SIZE=2>(State or other jurisdiction<BR>
of incorporation)</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="32%" ALIGN="CENTER"><FONT SIZE=2><B>0-27188<BR> </B></FONT><FONT SIZE=2>(Commission<BR>
File Number)</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="32%" ALIGN="CENTER"><FONT SIZE=2><B>33-0557266<BR> </B></FONT><FONT SIZE=2>(I.R.S.&nbsp;Employer<BR>
Identification&nbsp;No.)</FONT></TD>
</TR>
<TR VALIGN="TOP">
<TD COLSPAN=3 ALIGN="CENTER"><FONT SIZE=2><BR>
<BR></FONT> <FONT SIZE=2><B>PO Box 5350, Princeton, New Jersey<BR> </B></FONT><FONT SIZE=2>(Address of principal executive offices)</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="32%"><BR><FONT SIZE=2><B>08543-5350<BR> </B></FONT><FONT SIZE=2>(Zip Code)</FONT></TD>
</TR>
</TABLE>
<!-- end of user-specified TAGGED TABLE -->

<P ALIGN="CENTER"><FONT SIZE=2><B>(609)&nbsp;452-3600<BR>  </B></FONT><FONT SIZE=2>(Registrant's telephone number, including area code) </FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2><B>Not Applicable<BR>  </B></FONT><FONT SIZE=2>(Former name, former address and former fiscal year, if changed since last report) </FONT></P>

<P><FONT SIZE=2><hr
noshade width=100% align=left size=1>
<hr noshade width=100% align=left size=4> </FONT></P>

<HR NOSHADE>
<P style='page-break-before:always'></p>
<!-- ZEQ.=1,SEQ=1,EFW="2134150",CP="PHARMACOPEIA, INC.",DN="1",CHK=892043,FOLIO='blank',FILE='DISK008:[04SAN3.04SAN1173]BA1173A.;6',USER='AGAETZ',CD='20-APR-2004;11:28' -->
<!-- THIS IS THE END OF A COMPOSITION COMPONENT -->

<P><FONT SIZE=2><B>Item 5. OTHER EVENTS AND REGULATION FD DISCLOSURE  </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;On April&nbsp;19, 2004, Pharmacopeia,&nbsp;Inc. (the "Company") issued a press release announcing the that the Securities and Exchange Commission has declared
effective the registration statement on Form&nbsp;10 of Pharmacopeia Drug Discovery,&nbsp;Inc. ("PDD"), which is the drug discovery business being spun off by the Company. As previously announced
by the Company, the Board of Directors of the Company has set the record and distribution dates for a dividend, which will distribute to stockholders of the Company one share of PDD common stock for
every two shares of Company common stock held. This dividend is expected to occur on April&nbsp;30, 2004. Information statements regarding the distribution will be mailed to the Company's
stockholders of record as of the close of business on April&nbsp;16, 2004. PDD common stock is expected to begin trading on a "when-issued" basis on The Nasdaq National Market on
April&nbsp;20, 2004 under the ticker symbol "PCOPV." A copy of the Company's press release is furnished as an exhibit to this report. </FONT></P>

<P><FONT SIZE=2><B>Item 7. FINANCIAL STATEMENTS AND EXHIBITS  </B></FONT></P>

<DL compact>
<DT style='margin-bottom:-11pt;'><FONT SIZE=2>(c)</FONT></DT><DD><FONT SIZE=2>Exhibits. </FONT></DD></DL>
<BR>

<!-- User-specified TAGGED TABLE -->
<TABLE WIDTH="76%" BORDER=0 CELLSPACING=0 CELLPADDING=0>
<TR VALIGN="BOTTOM">
<TH WIDTH="12%" ALIGN="CENTER"><FONT SIZE=1><B>Exhibit Number</B></FONT><HR NOSHADE></TH>
<TH WIDTH="3%"><FONT SIZE=1>&nbsp;</FONT></TH>
<TH WIDTH="85%" ALIGN="CENTER"><FONT SIZE=1><B>Description</B></FONT><HR NOSHADE></TH>
</TR>
<TR VALIGN="TOP">
<TD WIDTH="12%" ALIGN="RIGHT"><FONT SIZE=2>99.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="85%"><FONT SIZE=2>Press Release dated April 19, 2004</FONT></TD>
</TR>
</TABLE>
<!-- end of user-specified TAGGED TABLE -->

<HR NOSHADE>
<P style='page-break-before:always'></p>
<!-- ZEQ.=1,SEQ=2,EFW="2134150",CP="PHARMACOPEIA, INC.",DN="1",CHK=677245,FOLIO='blank',FILE='DISK008:[04SAN3.04SAN1173]DE1173A.;6',USER='AGAETZ',CD='20-APR-2004;09:07' -->
<!-- THIS IS THE END OF A COMPOSITION COMPONENT -->
<!-- TOC_END -->
<P ALIGN="CENTER"><FONT SIZE=2><A
NAME="jc1173_signatures"> </A>
<A NAME="toc_jc1173_1"> </A>
<BR></FONT><FONT SIZE=2><B>Signatures    <BR>    </B></FONT></P>


<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned
hereunto duly authorized. </FONT></P>

<UL>
<UL>
<UL>
<UL>
<UL>
<UL>
<UL>
<UL>
<UL>
<UL>
<UL>

<P><FONT SIZE=2>PHARMACOPEIA,&nbsp;INC.
</FONT></P>

<P><FONT SIZE=2>By:
/s/&nbsp;&nbsp;</FONT><FONT SIZE=2>JOHN J. HANLON</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT></P>

<P><FONT SIZE=2>John
J. Hanlon, Executive Vice President and<BR>
Chief Financial Officer </FONT></P>

</UL>
</UL>
</UL>
</UL>
</UL>
</UL>
</UL>
</UL>
</UL>
</UL>
</UL>

<P><FONT SIZE=2>Date:
April&nbsp;20, 2004 </FONT></P>

<HR NOSHADE>
<P style='page-break-before:always'></p>
<!-- ZEQ.=1,SEQ=3,EFW="2134150",CP="PHARMACOPEIA, INC.",DN="1",CHK=185715,FOLIO='blank',FILE='DISK008:[04SAN3.04SAN1173]JC1173A.;4',USER='AGAETZ',CD='20-APR-2004;09:06' -->
<!-- THIS IS THE END OF A COMPOSITION COMPONENT -->
<BR>
<P><br><A NAME="04SAN1173_1">QuickLinks</A><br></P><!-- TOC_BEGIN -->
<FONT SIZE=2><A HREF="#toc_jc1173_1">Signatures</A></FONT><BR>
<!-- SEQ=,FILE='QUICKLINK',USER=SFLORES,SEQ=,EFW="2134150",CP="PHARMACOPEIA, INC.",DN="1" -->
<!-- TOCEXISTFLAG -->
</BODY>
</HTML>

</TEXT>
</DOCUMENT>
<DOCUMENT>
<TYPE>EX-99.1
<SEQUENCE>3
<FILENAME>a2134150zex-99_1.htm
<DESCRIPTION>EXHIBIT 99.1
<TEXT>
<HTML>
<HEAD>

</HEAD>
<BODY BGCOLOR="#FFFFFF" LINK=BLUE  VLINK=PURPLE>
<BR>
<FONT SIZE=3 ><A HREF="#04SAN1173_2">QuickLinks</A></FONT>
<font size=3> -- Click here to rapidly navigate through this document</font>
<!-- TOC_END -->
<P ALIGN="RIGHT"><FONT SIZE=2><B>Exhibit&nbsp;99.1  </B></FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2><A
NAME="kc1173_pharmacopeia_announces_effecti__pha04017"> </A>
<A NAME="toc_kc1173_1"> </A>
<BR></FONT><FONT SIZE=2><B>PHARMACOPEIA ANNOUNCES EFFECTIVENESS OF FORM 10 REGISTRATION STATEMENT OF PHARMACOPEIA DRUG DISCOVERY    <BR>    </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Princeton, New Jersey, April&nbsp;19, 2004&#151;Pharmacopeia,&nbsp;Inc. (Nasdaq: ACCL) today announced that the Securities and Exchange Commission has
declared the registration statement on Form&nbsp;10 of Pharmacopeia Drug Discovery,&nbsp;Inc. (PDD) effective, which is a condition to the completion of the spin-off of PDD to
Pharmacopeia stockholders. As previously announced, the Board of Directors of Pharmacopeia has set the record and distribution dates for a dividend that will distribute to Pharmacopeia stockholders
one share of PDD common stock for every two shares of Pharmacopeia common stock held. Fractional shares will not be distributed but will be aggregated and sold in the public market. The net cash
proceeds of these sales will be distributed ratably to those stockholders who would have otherwise received fractional shares. This dividend is expected to occur on April&nbsp;30, 2004. Information
statements regarding the distribution will be mailed to Pharmacopeia stockholders of record as of the close of business on April&nbsp;16, 2004. Pharmacopeia stockholders will not be required to take
any action to receive the PDD common stock on the distribution date. </FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The
dividend is intended to qualify as a tax-free distribution to Pharmacopeia stockholders for U.S. federal income tax purposes (except for cash received in lieu of any
fractional share interest). Payment of the dividend is subject to the satisfaction or waiver of certain conditions, including Pharmacopeia's receiving an opinion of counsel regarding the
tax-free nature of the distribution. </FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;PDD
common stock is expected to begin trading on a "when-issued" basis on The Nasdaq National Market on April&nbsp;20, 2004 under the ticker symbol "PCOPV." During the
"when-issued" trading period, from April&nbsp;20, 2004 through the distribution date, which is expected to be April&nbsp;30, 2004, Pharmacopeia common stock will continue to include
the right to receive PDD common stock and will trade on The Nasdaq National Market under the current ticker "ACCL." </FONT></P>


<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pharmacopeia
(www.pharmacopeia.com) is a leader in enabling science and technology that accelerates and improves the drug discovery and chemical development processes. PDD integrates
proprietary small molecule combinatorial and medicinal chemistry, high-throughput screening, in-vitro pharmacology, computational methods and informatics to discover and
optimize lead compounds. Pharmacopeia's software subsidiary, Accelrys, develops and commercializes molecular modeling and simulation software for the life sciences and materials research markets,
cheminformatics
and decision support systems, and bioinformatics tools including gene sequence analysis. PDD is headquartered in Princeton, New Jersey. Accelrys is headquartered in San Diego, California. </FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2>### </FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT><FONT
SIZE=2><I>When used anywhere in this document, the words "expects", "believes", "anticipates", "estimates" and similar expressions are intended to identify forward-looking
statements. Forward-looking statements herein may include statements addressing future financial and operating results of Pharmacopeia. Pharmacopeia has based these forward-looking statements on its
current expectations about future events. Such statements are subject to risks and uncertainties including, but not limited to, the successful implementation of Pharmacopeia's strategic plans, the
acceptance of new products, the obsolescence of existing products, the resolution of existing and potential future patent issues, additional competition, changes in economic conditions, completion of
the spin-off of PDD and other risks described in documents Pharmacopeia has filed with the Securities and Exchange Commission, including its most recent report on
Form&nbsp;10-K and subsequent reports on Form&nbsp;10-Q, and the registration statement on Form&nbsp;10 that PDD has filed with the Securities and Exchange Commission.
All forward-looking statements in this document are qualified entirely by the cautionary statements included in this document and such filings. These risks and uncertainties could cause actual results
to differ materially from results expressed or implied by forward-looking statements contained in this document. These forward-looking statements speak only as of the date of this document.
Pharmacopeia disclaims any undertaking to publicly update or revise any forward-looking statements  </I></FONT></P>

<HR NOSHADE>
<P style='page-break-before:always'></p>
<!-- ZEQ.=1,SEQ=1,EFW="2134150",CP="PHARMACOPEIA, INC.",DN="2",CHK=143321,FOLIO='blank',FILE='DISK008:[04SAN3.04SAN1173]KC1173A.;4',USER='AGAETZ',CD='20-APR-2004;09:08' -->
<BR>

<P><FONT SIZE=2><I> contained herein to reflect any change in its expectations with regard thereto or any change in events, conditions or circumstances on which any such statement is based.</I></FONT></P>

<P><FONT SIZE=2>Pharmacopeia/Accelrys
Contact: </FONT></P>

<P><FONT SIZE=2>John
J. Hanlon<BR>
Chief Financial Officer<BR>
Pharmacopeia, Inc.<BR>
(609) 452-3600<BR></FONT> <FONT SIZE=2><I>irreq@pharmacopeia.com</I></FONT></P>

<P><FONT SIZE=2>PDD
Contact: </FONT></P>

<P><FONT SIZE=2>Brian
M. Posner<BR>
Vice President, Finance<BR>
Pharmacopeia Drug Discovery, Inc.<BR>
(609) 452-3600 </FONT></P>

<HR NOSHADE>
<P style='page-break-before:always'></p>
<!-- ZEQ.=2,SEQ=2,EFW="2134150",CP="PHARMACOPEIA, INC.",DN="2",CHK=614489,FOLIO='blank',FILE='DISK008:[04SAN3.04SAN1173]KC1173A.;4',USER='AGAETZ',CD='20-APR-2004;09:08' -->
<!-- THIS IS THE END OF A COMPOSITION COMPONENT -->
<BR>
<P><br><A NAME="04SAN1173_2">QuickLinks</A><br></P><!-- TOC_BEGIN -->
<FONT SIZE=2><A HREF="#toc_kc1173_1">PHARMACOPEIA ANNOUNCES EFFECTIVENESS OF FORM 10 REGISTRATION STATEMENT OF PHARMACOPEIA DRUG DISCOVERY</A></FONT><BR>
<!-- SEQ=,FILE='QUICKLINK',USER=SFLORES,SEQ=,EFW="2134150",CP="PHARMACOPEIA, INC.",DN="2" -->
<!-- TOCEXISTFLAG -->
</BODY>
</HTML>

</TEXT>
</DOCUMENT>
</SUBMISSION>
