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<ACCESSION-NUMBER>0001047469-04-011479
<TYPE>8-K
<PUBLIC-DOCUMENT-COUNT>2
<PERIOD>20040407
<ITEMS>12
<ITEMS>5
<ITEMS>7
<FILING-DATE>20040409
<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>04726701
</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>a2133227z8-k.htm
<DESCRIPTION>FORM 8-K
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<FONT SIZE=3 ><A HREF="#04SAN1153_1">QuickLinks</A></FONT>
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<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=2><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): </FONT><FONT SIZE=2><B>April&nbsp;7, 2004  </B></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>

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<TD WIDTH="33%" ALIGN="CENTER"><FONT SIZE=2><B>Delaware</B></FONT><FONT SIZE=2><BR>
(State or other jurisdiction of<BR>
incorporation or organization)</FONT></TD>
<TD WIDTH="33%" ALIGN="CENTER"><FONT SIZE=2><B>0-27118</B></FONT><FONT SIZE=2><BR>
(Commission<BR>
File Number)</FONT></TD>
<TD WIDTH="33%" ALIGN="CENTER"><FONT SIZE=2><B>33-0557266</B></FONT><FONT SIZE=2><BR>
(I.R.S. Employer<BR>
Identification No.)</FONT></TD>
</TR>
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<TD WIDTH="67%" ALIGN="CENTER"><BR><FONT SIZE=2><B>PO Box 5350, Princeton, New Jersey</B></FONT><FONT SIZE=2><BR>
(Address of principal executive offices)</FONT></TD>
<TD WIDTH="33%" ALIGN="CENTER"><BR><FONT SIZE=2><B>08543-5350</B></FONT><FONT SIZE=2><BR>
(Zip Code)</FONT></TD>
</TR>
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<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
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<P><FONT SIZE=2><A
NAME="de1153_item_5._other_events_and_regulation_fd_disclosure"> </A>
<A NAME="toc_de1153_1"> </A>
<BR></FONT><FONT SIZE=2><B>Item 5. OTHER EVENTS AND REGULATION FD DISCLOSURE    <BR>    </B></FONT></P>

<P><FONT SIZE=2>On
April&nbsp;7, 2004, Pharmacopeia,&nbsp;Inc. (the "Company") issued a press release announcing that the proposed spin-off of its Pharmacopeia Drug Discovery,&nbsp;Inc. unit is
expected to occur by the end of April&nbsp;2004. A copy of the Company's press release is furnished as an exhibit to this report. </FONT></P>


<P><FONT SIZE=2><A
NAME="de1153_item_7._financial_statements_and_exhibits"> </A>
<A NAME="toc_de1153_2"> </A>
<BR></FONT><FONT SIZE=2><B>Item 7. FINANCIAL STATEMENTS AND EXHIBITS    <BR>    </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>

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<TH WIDTH="3%"><FONT SIZE=1>&nbsp;</FONT></TH>
<TH WIDTH="85%" ALIGN="CENTER"><FONT SIZE=1><B>Description</B></FONT><HR NOSHADE></TH>
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<TD WIDTH="12%" ALIGN="CENTER"><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 7, 2004</FONT></TD>
</TR>
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<P><FONT SIZE=2><A
NAME="de1153_item_12._results_of_ope__de102072"> </A>
<A NAME="toc_de1153_3"> </A>
<BR></FONT><FONT SIZE=2><B>Item 12. RESULTS OF OPERATIONS AND FINANCIAL CONDITION    <BR>    </B></FONT></P>

<P><FONT SIZE=2>On
April&nbsp;7, 2004, the Company issued a press release announcing certain financial results for the quarterly period ended March&nbsp;31, 2004. A copy of the Company's press release is
furnished as an exhibit to this report. </FONT></P>

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<P ALIGN="CENTER"><FONT SIZE=2><A
NAME="jc1153_signatures"> </A>
<A NAME="toc_jc1153_1"> </A>
<BR></FONT><FONT SIZE=2><B>Signatures    <BR>    </B></FONT></P>

<P><FONT SIZE=2>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>

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<TD WIDTH="47%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD COLSPAN=3><FONT SIZE=2>PHARMACOPEIA,&nbsp;INC.</FONT></TD>
</TR>
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<TD WIDTH="47%"><FONT SIZE=2><BR>
&nbsp;</FONT></TD>
<TD WIDTH="5%"><FONT SIZE=2><BR>
By:</FONT></TD>
<TD WIDTH="1%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="47%"><FONT SIZE=2><BR>
/s/&nbsp;&nbsp;</FONT><FONT SIZE=2>JOHN J. HANLON</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT></TD>
</TR>
<TR VALIGN="TOP">
<TD WIDTH="47%"><FONT SIZE=2><BR>
&nbsp;</FONT></TD>
<TD COLSPAN=3><FONT SIZE=2><BR>
John J. Hanlon,<BR>
Executive Vice President and Chief Financial Officer</FONT></TD>
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<P><FONT SIZE=2>Date:
April&nbsp;9, 2004 </FONT></P>

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<BR>
<P><br><A NAME="04SAN1153_1">QuickLinks</A><br></P><!-- TOC_BEGIN -->
<UL>
<FONT SIZE=2><A HREF="#toc_de1153_1">Item 5. OTHER EVENTS AND REGULATION FD DISCLOSURE</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_de1153_2">Item 7. FINANCIAL STATEMENTS AND EXHIBITS</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_de1153_3">Item 12. RESULTS OF OPERATIONS AND FINANCIAL CONDITION</A></FONT><BR>
</UL>
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<FONT SIZE=2><A HREF="#toc_jc1153_1">Signatures</A></FONT><BR>
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<TYPE>EX-99.1
<SEQUENCE>3
<FILENAME>a2133227zex-99_1.htm
<DESCRIPTION>EXHIBIT 99.1
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<P ALIGN="RIGHT"><FONT SIZE=2><A
NAME="ke1153_exhibit_99.1"> </A>
<A NAME="toc_ke1153_1"> </A>
<BR></FONT><FONT SIZE=2><B>Exhibit&nbsp;99.1    <BR>    </B></FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2><A
NAME="ke1153_pharmacopeia_announces_update___pha03710"> </A>
<A NAME="toc_ke1153_2"> </A>
<BR></FONT><FONT SIZE=2><B>PHARMACOPEIA ANNOUNCES UPDATE ON TIMING OF<BR>  PROPOSED "SPIN-OFF" OF PHARMACOPEIA DRUG DISCOVERY    <BR>    </B></FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2><B>Company also comments on first quarter 2004,<BR>
and provides full-year financial guidance  </B></FONT></P>

<P><FONT SIZE=2>Princeton,
New Jersey, April&nbsp;7, 2004&#151;Pharmacopeia,&nbsp;Inc. (Nasdaq: ACCL) today announced that the proposed spin-off of its Pharmacopeia Drug Discovery,&nbsp;Inc.
(PDD) unit is expected to occur by the end of April&nbsp;2004. The Pharmacopeia Board of Directors intends to meet next week to consider final approval of the pro rata distribution to stockholders
of 100% of the common stock of PDD. Subject to final Nasdaq approval, PDD common stock will trade under the symbol "PCOP" upon completion of the spin-off. Pharmacopeia will continue to
trade under the symbol "ACCL" after the distribution and, subject to stockholder approval at its upcoming annual meeting, the company will change its name to "Accelrys" to better
reflect its focus on the scientific software business. The transaction remains subject to Pharmacopeia's receipt of regulatory approvals and a favorable tax opinion, market conditions and final
approval by the Pharmacopeia Board. </FONT></P>

<P><FONT SIZE=2>The
Company also announced that consolidated revenue for the quarter ended March&nbsp;31, 2004 was approximately 34% lower than in the first quarter of 2003. In addition to the anticipated negative
effect on revenue of the new subscription software license offered in the first quarter, Accelrys revenue in the quarter was impacted by a 22% decrease in orders as compared to the 2003 first quarter.
The Company attributed the shortfall at Accelrys to, among other issues, confusion regarding the change to the new subscription licensing contracts and some disruption associated with the planned
spin-off of PDD. PDD revenue for the quarter ended March&nbsp;31, 2004 decreased approximately 28% as compared to the 2003 first quarter, due principally to lower milestone revenue and
reduced third party collaborative research funding. </FONT></P>

<P><FONT SIZE=2>In
spite of lower revenue and orders at Accelrys in the first quarter, total deferred revenue, which includes unbilled orders, in the software unit grew to more than $47&nbsp;million at
March&nbsp;31, 2004, a 19% increase over the level at March&nbsp;31, 2003. Further, on a consolidated basis, the benefits from recent and continuing cost containment initiatives were reflected in
the Company's improved cash position at the end of the 2004 first quarter. The Company's cash and cash equivalents at March&nbsp;31, 2004 grew to more than $141&nbsp;million, over a
$7&nbsp;million increase from its December&nbsp;31, 2003 level. </FONT></P>

<P><FONT SIZE=2>With
regard to financial guidance, John Hanlon, Pharmacopeia's Chief Financial Officer, said, "As we have stated in our previous releases and conference calls, we do not believe the first calendar
quarter is a good indicator of the Company's actual performance over the balance of the year. Consistent with this view, we expect Accelrys orders for the period beginning April&nbsp;1, 2004 and
ending March&nbsp;31, 2005 (the software division's 2005 fiscal year) to increase modestly over orders for the twelve months ended March&nbsp;31, 2004. We anticipate a market environment in fiscal
2005 that will continue to improve gradually, which we believe will help us drive new sales and continue to build our deferred revenue base. Further, we see revenue potential from the activities of
our Business Development Group, recently established by Accelrys to pursue in-licensing, out-licensing and merger and acquisition opportunities. Due to the accounting for
Accelrys' new subscription license offering, we expect revenue recorded for fiscal 2005 will be from 12% to 15% lower than in the comparable twelve month period ended March&nbsp;31, 2004. We expect
cash flow from operations to be higher in fiscal 2005 than in the twelve months ended March&nbsp;31, 2004. We believe this improvement in cash flow at Accelrys will be a product of both its lower
operating expense base and its customers' adoption of the new subscription license offering on payment terms consistent with historical practice." </FONT></P>


<P><FONT SIZE=2>"We
intend to increase our level of internal, self-funded research at PDD over the remainder of 2004, as we believe such proprietary programs have the potential to generate higher future
returns for PDD than are typical in the drug discovery unit's standard collaborative agreements. Notwithstanding this </FONT></P>

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<P><FONT SIZE=2>enhanced
investment in PDD's own programs, however, we do not expect PDD's net utilization of cash during the remainder of calendar year 2004 to exceed $5.0&nbsp;million." </FONT></P>

<P><FONT SIZE=2>"Consistent
with our previous guidance, the Company will record one-time charges in the quarter ended March&nbsp;31, 2004 estimated at between $11&nbsp;million and $12&nbsp;million
in total. These charges primarily reflect costs incurred in connection with the spin-off, the consolidation of facilities at PDD and the reduction of staff implemented in
January&nbsp;2004 at Accelrys." </FONT></P>

<P><FONT SIZE=2>Pharmacopeia
(www.pharmacopeia.com) is a leader in enabling science and technology that accelerates and improves the drug discovery and chemical development processes. Pharmacopeia's Drug Discovery
business (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. Pharmacopeia is headquartered in Princeton, New Jersey. </FONT></P>

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

<P><FONT SIZE=1><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. 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 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>Contact:<BR>
<BR>
John J. Hanlon<BR>
Chief Financial Officer<BR>
Pharmacopeia, Inc.<BR>
(609) 452-3600<BR>
irreq@pharmacopeia.com </FONT></P>

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<BR>
<P><br><A NAME="04SAN1153_2">QuickLinks</A><br></P><!-- TOC_BEGIN -->
<UL>
<FONT SIZE=2><A HREF="#toc_ke1153_1">Exhibit 99.1</A></FONT><BR>
</UL>
<FONT SIZE=2><A HREF="#toc_ke1153_2">PHARMACOPEIA ANNOUNCES UPDATE ON TIMING OF PROPOSED "SPIN-OFF" OF PHARMACOPEIA DRUG DISCOVERY</A></FONT><BR>

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