<PAGE>
 
                      SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C. 20549

                                   FORM 10-Q

(Mark One)
     [X]  QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES 
          EXCHANGE ACT OF 1934

     For the quarterly period ended June 30, 1997

                                      or

     [_]  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES 
          EXCHANGE ACT OF 1934

                        Commission File Number: 0-27118
                                                -------

                              PHARMACOPEIA, INC.

--------------------------------------------------------------------------------
             (Exact name of registrant as specified in its charter

Delaware                                                 33-0557266
--------------------------------------------------------------------------------
(State or other jurisdiction of             (I.R.S. Employer Identification No.)
incorporation or organization

101 College Road East, Princeton, New Jersey                        08540
--------------------------------------------------------------------------------
(Address of principal executive offices)                         (Zip code)

                                 (609) 452-3600
--------------------------------------------------------------------------------
             (Registrant's telephone number, including area code)

                                Not Applicable
--------------------------------------------------------------------------------
(Former name, former address and former fiscal year, if changed since last 
                                    report)

Indicate by check mark whether the registrant (1) has filed all reports required
to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during
the preceding 12 months (or such shorter period that the registrant was required
to file such reports) and (2) has been subject to such filing requirements for 
the past 90 days-- Yes  X    No___
                       ---

Indicate the number of shares outstanding of each of the issuer's classes of 
common stock, as of the latest practicable date:


               CLASS                         OUTSTANDING AT JULY 31, 1997
   ------------------------------       -------------------------------------
   Common Stock, $.0001 par value                   11,561,098
<PAGE>
 
                              PHARMACOPEIA, INC.

                                   FORM 10-Q

                               TABLE OF CONTENTS

<TABLE> 
<CAPTION> 
ITEM                                                                     PAGE
----                                                                     ----
<S>                                                                      <C> 
PART 1. FINANCIAL INFORMATION

Item 1.        Financial Statements:
          
               Balance Sheets-June 30, 1997 and December 31, 1996          3

               Statements of Operations-Three and Six Months Ended         4
               June 30, 1997 and 1996             

               Statements of Cash Flows-Six Months Ended                   5
               June 30, 1997 and 1996

               Notes to Financial Statements                               6

Item 2.        Management's Discussion and Analysis of Financial          7-9
               Condition and Results of Operations
          
PART II. OTHER INFORMATION               

Item 2.        Changes in Securities                                      10 

Item 4.        Submission of Matters to a Vote of Security Holders       10-11

Item 6.        Exhibits and Reports on Form 8-K                          12-13

SIGNATURE                                                                 14

INDEX TO EXHIBITS                                                         15
</TABLE> 

                                      -2-
<PAGE>
 
                                    PART 1
                             FINANCIAL INFORMATION


ITEM 1. FINANCIAL STATEMENTS

                              PHARMACOPEIA, INC.
                                BALANCE SHEETS
                   (DOLLARS IN THOUSANDS, EXCEPT SHARE DATA)

<TABLE> 
<CAPTION> 
                                                                        JUNE 30,      DECEMBER 31,                
                                                                          1997           1996
                                                                        ---------------------------                
                                                                        (UNAUDITED)
<S>                                                                     <C>            <C> 
ASSETS
 Current assets:
  Cash and cash equivalents                                             $    5,803     $    17,059   
  Marketable securities                                                     53,056          64,423                 
  Prepaid expenses and other current assets                                  2,072           1,525                 
                                                                        ---------------------------                
Total current assets                                                        60,931          83,007                 
                                                                        ---------------------------                
                                                                                                                   
Non-current investments in marketable securities                            19,088                                 
Property and equipment, net                                                 10,013           8,295                 
Other assets                                                                   342             677                 
                                                                        ---------------------------                
                                                                        $   90,374     $    91,979                 
                                                                        ===========================                 
                                                                                                                   
LIABILITIES AND STOCKHOLDERS' EQUITY                                                                              
 Current liabilities:                                                                                              
  Accounts payable                                                      $      830     $       742                 
  Accrued liabilities                                                        2,132           2,240                 
  Notes payable, current portion                                               678             710                 
  Deferred revenue                                                          13,060          15,088                 
                                                                        ---------------------------                
Total current liabilities                                                   16,700          18,780                 
                                                                                                                   
Notes payable, long-term portion                                             1,078           1,405                 
Deferred revenue, long-term                                                  1,614           2,046                 
                                                                                                                   
Commitments                                                                                                       
                                                                                                                   
Stockholders' equity:                                                                                             
  Preferred stock, $.0001 par value; 2,000,000 shares authorized;                                                  
   none issued and outstanding                                                                                      
  Common stock, $.0001 par value; 40,000,000 shares authorized;                                                    
   11,557,004 and 11,267,499 shares issued and outstanding at                                                      
   June 30, 1997 and December 31, 1996, respectively                             1               1                 
  Additional paid-in capital                                               101,883          97,542                 
  Accumulated deficit                                                      (30,902)        (27,795)                
                                                                        ---------------------------                
Total stockholders' equity                                                  70,982          69,748                 
                                                                        ---------------------------                
                                                                        $   90,374     $    91,979                 
                                                                        ===========================                 
</TABLE> 

        See accompanying notes to these unaudited financial statements.

                                      -3-
<PAGE>
 
                              PHARMACOPEIA, INC.

                           STATEMENTS OF OPERATIONS
                 (DOLLARS IN THOUSANDS, EXCEPT PER SHARE DATA)


<TABLE> 
<CAPTION> 
                                        THREE MONTHS ENDED JUNE 30,    SIX MONTHS ENDED JUNE 30,
                                            1997          1996            1997          1996
                                        ---------------------------    -------------------------
                                                (UNAUDITED)                   (UNAUDITED)

<S>                                     <C>           <C>              <C>          <C> 
Contract revenue                            $5,586        $2,847          $11,518       $4,854

Operating expenses:
 Research and development:
  Collaborative                              4,178         2,680            8,329        4,887
  Proprietary                                2,821         1,890            5,550        3,740
 General and administrative                  1,319         1,163            2,777        2,570
                                        ---------------------------    -------------------------
Operating loss                              (2,732)       (2,886)          (5,138)      (6,343)

Interest income                              1,096         1,004            2,160        1,883
Interest expense                               (61)          (63)            (128)        (114)
                                        ---------------------------    -------------------------
Net loss                                   $(1,697)      $(1,945)         $(3,106)     $(4,574)
                                        ---------------------------    -------------------------

Net loss per share                           $(.15)        $(.18)           $(.27)       $(.43)
                                        ===========================    =========================

Weighted-average number of
common shares outstanding
during the period                       11,371,134    10,852,144       11,320,723   10,671,341
                                        ===========================    =========================
</TABLE> 

        See accompanying notes to these unaudited financial statements.

                                      -4-
<PAGE>
 
                              PHARMACOPEIA, INC.

                           STATEMENTS OF CASH FLOWS
                            (DOLLARS IN THOUSANDS)

<TABLE> 
<CAPTION> 
                                                                               SIX MONTHS ENDED JUNE 30,
                                                                                  1997          1996    
                                                                            ------------------------------- 
                                                                                     (UNAUDITED)        
<S>                                                                         <C>             <C> 
CASH FLOWS FROM OPERATING ACTIVITIES                                    
Net loss                                                                    $     (3,106)   $    (4,574)
Adjustments to reconcile net loss to net cash provided                  
     by (used in) operating activities:                                 
     Depreciation                                                                  1,216            559
     Amortization                                                                     20             20
     Changes in operating assets and liabilities:                                 
     (Increase) in prepaid expenses and other current assets                        (547)          (664)
     (Increase) decrease in other assets                                             314           (111)
     Increase in accounts payable                                                     88            517 
     (Decrease) in accrued liabilities                                              (108)          (250)
     Increase (decrease) in deferred revenue                                      (2,460)         6,738  
                                                                            ------------------------------- 
Net cash provided by (used in) operating activities                               (4,583)         2,235
                                                                        
CASH FLOWS FROM INVESTING ACTIVITIES                                    
Capital expenditures                                                              (2,934)        (4,802)
Purchase of marketable securities                                                (53,174)       (52,697)
Proceeds from sales of marketable securities                                      45,453         36,021
                                                                            ------------------------------- 
Net cash used in investing activities                                            (10,655)       (21,478)
                                                                        
CASH FLOWS FROM FINANCING ACTIVITIES                                    
Net proceeds from issuance of common stock                                         4,341         18,637
Increase in notes payable                                                                         1,344
Repayments of notes payable                                                         (359)          (264)
                                                                            ------------------------------- 
Net cash provided by financing activities                                          3,982         19,717
                                                                            ------------------------------- 
Increase (decrease) in cash and cash equivalents                                 (11,256)           474
Cash and cash equivalents at beginning of period                                  17,059         28,612
                                                                            ------------------------------- 
Cash and cash equivalents at end of period                                  $      5,803    $    29,086
                                                                            ===============================
</TABLE> 

        See accompanying notes to these unaudited financial statements.

                                      -5-
<PAGE>
 
                              PHARMACOPEIA, INC.

                         NOTES TO FINANCIAL STATEMENTS
                                  (UNAUDITED)


NOTE (1)-- BASIS OF PRESENTATION

     The unaudited financial statements have been prepared in accordance with 
generally accepted accounting principles for interim financial information. 
Accordingly, they do not include all of the information and footnotes required 
by generally accepted accounting principles for complete financial statements. 
In the opinion of management, all adjustments (consisting of normal recurring 
accruals) considered necessary for a fair presentation have been included. 
Interim results are not necessarily indicative of the results that may be 
expected for the year. For further information, refer to the financial 
statements and footnotes thereto included in the Company's Annual Report on Form
10-K for the year ended December 31, 1996.

NOTE (2)-- NET LOSS PER COMMON SHARE

     Net loss per common share is based on net loss for the relevant period 
divided by the weighted average number of shares issued and outstanding during 
the period. Stock options and common stock issuable upon conversion of warrants 
are not reflected as their effect would be antidilutive for both primary and 
fully diluted earnings per share computations.

     In February 1997, the Financial Accounting Standard Board issued Statement 
No. 128, Earnings per Share, which is required to be adopted on December 31, 
1997. At that time, the Company will be required to change the method currently 
used to compute earnings per share and to restate all prior periods. The impact 
of statement 128 on the calculation of primary and fully diluted earnings per 
share is not expected to be material.

                                      -6-
<PAGE>
 
ITEM 2. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS 
        OPERATIONS

OVERVIEW

     Pharmacopeia, Inc. ("Pharmacopeia" or the "Company") was incorporated in 
March 1993 and is engaged in research and development and chemical library 
production for collaborations and for its own use. The Company's research and 
development has focused on efficient, cost effective, high throughput systems 
for synthesizing and screening large libraries of chemicals for new drug 
discovery and optimization. The Company has incurred losses since inception and,
as of June 30, 1997 had an accumulated deficit of $30.9 million. The Company 
anticipates incurring additional losses over at least the next several years as 
it expands its research and development and chemical library production efforts.
The Company expects that its losses will fluctuate from quarter to quarter and
that such variations may be substantial.

RESULTS OF OPERATIONS

     The Company expects that its revenue sources for at least the next several 
years will be limited to future drug discovery collaboration payments from 
Schering Corporation and Schering-Plough Ltd. (together, "Schering-Plough"), 
Berlex Laboratories, Inc. ("Berlex"), Novartis Corporation ("Novartis"), Bayer 
Corporation ("Bayer"), Daiichi Pharmaceutical Co., Ltd. ("Daiichi"), and Akzo 
Nobel/Organon ("Organon") and from other customers under existing arrangements 
and others that may be entered into in the future. The timing and amounts of 
such revenues, if any, will likely fluctuate. Historical results should not be 
viewed as indicative of future operating results. The Company will be required 
to conduct significant research, development and production activities during 
the next several years to fulfill its obligations under the Schering-Plough, 
Berlex, Novartis, Bayer, Daiichi and Organon drug discovery collaborative 
agreements and to develop other collaborations and technologies. The Company
does not anticipate having net income in the next several years.

THREE AND SIX MONTHS ENDED JUNE 30, 1997 AND 1996

     Revenues for the three and six months ended June 30, 1997 increased to $5.6
million and $11.5 million, respectively, compared to $2.8 million and $4.9 
million for the comparable periods in 1996. The increase in 1997 revenues 
primarily reflects expanded efforts in the drug discovery collaborations with 
Bayer, Daiichi, Organon and Novartis and the achievement of certain milestones 
with Berlex and Schering-Plough during the first quarter of 1997.

                                      -7-
<PAGE>
 
     Research and development expenses increased to $7.0 million and $13.9 
million for the three and six months ended June 30, 1997, respectively, compared
to $4.6 million and $8.6 million for the corresponding periods in 1996. These 
increased amounts primarily reflect increased salaries and personnel expenses as
the Company continued to hire additional research and development personnel, 
equipment depreciation, leasehold amortization, and laboratory supplies
purchased in connection with the expansion of the Company's chemical library
production and screening efforts for drug discovery collaborations and for
internal discovery programs.

     General and administrative expenses increased to $1.3 million and $2.8 
million for the three and six months ended June 30, 1997, respectively, compared
to $1.2 million and $2.6 million for the same periods in 1996. The increase is 
primarily attributable to increased payroll and personnel expenses as the 
Company continued to hire additional management and administrative personnel, 
along with increased patent legal fees.

     The Company had interest income of $1.1 million and $2.2 million in the 
three and six months ended June 30, 1997, respectively, compared to $1.0 million
and $1.9 million for the comparable periods in 1996. The increase in interest
income resulted from higher average balances of cash, cash equivalents and
marketable securities. Interest expense for both periods is a result of interest
incurred on notes payable.

LIQUIDITY AND CAPITAL RESOURCES

     As of June 30, 1997, the Company had working capital of $44.2 million. The 
Company has funded its activities through June 30, 1997 primarily through the 
sale of equity securities and funding under collaborative arrangements. From 
inception through June 30, 1997, the Company received $101.9 million in net 
proceeds from equity financing and received $42.3 million in research and 
development, license fees and milestone payments under collaborative agreements.

     The Company's funds are currently invested in U.S. Treasury and government 
agency obligations, investment grade commercial paper and other short-term money
market instruments. The Company may also invest such proceeds in investment 
grade, interest-bearing securities having a maximum maturity of two years. As of
June 30, 1997, the Company's cash and cash equivalents totaled $5.8 million. 
In addition, the Company had marketable securities of $72.1 million.

     In connection with the Company's agreement with the Trustees of Columbia 
University and Cold Spring Harbor Laboratory, the Company is required to pay 
annual license fees. The Company is also required to pay to Columbia University 
certain royalties.

     In addition, as of June 30, 1997, the Company had outstanding commitments 
for construction and equipment purchases totaling $0.7 million. The Company 
anticipates that its capital requirements will continue at approximately the 
same level over the next two years as the Company expands it research and 
development activities. In connection with such expansion, the Company expects 
to incur substantial expenditures for hiring additional management, scientific 
and administrative personnel and for planned expansion and upgrading of its 
facilities, including acquisition of additional equipment.

                                      -8-
<PAGE>
 
     The Company anticipates that its existing capital resources will be 
adequate to fund the Company's operations at least through 1998. There can be no
assurance that changes will not occur that would consume available capital 
resources before such time. The Company's capital requirements depend on 
numerous factors, including the ability of the Company to enter into additional 
collaborative arrangements, competing technological and market developments, 
changes in the Company's existing collaborative relationships, the cost of 
filing, prosecuting, defending and enforcing patent claims and other 
intellectual property rights, the purchase of additional capital equipment, 
acquisitions of other businesses or technologies, the progress of the Company's 
drug discovery programs and the progress of the Company's customers' milestone 
and royalty producing activities. There can be no assurance that additional 
funding, if necessary, will be available on favorable terms, if at all. The 
Company's forecasts of the period of time through which its financial resources 
will be adequate to support its operations is forward looking information, and 
actual results could vary. The factors described earlier in this paragraph will 
impact the Company's future capital requirements and the adequacy of its 
available funds.

                                      -9-
<PAGE>
 
                                    PART II

                               OTHER INFORMATION

     ITEM 2. CHANGES IN SECURITIES

                   Transaction                   Number of       Aggregate
                       Date      Securities   Securities (1)  Offering Price
                  ------------  ------------  --------------  --------------
       Organon    May 31, 1997  Common Stock     276,707        $4,165,000

     (1)  Transaction exempt from the registration requirements of Section 5 of
          the Securities Act of 1933, as amended, by virtue of the exemption
          contained in Section 4(2) of such act.

     ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

(a)  The Annual Meeting of Stockholders was held on May 9, 1997.

(b)  The following persons were elected to continue as the directors of the 
     Company:

                              FOR             AGAINST
                            ---------      ------------
          Frank Baldino     8,297,824         46,581
          Edith W. Martin   8,297,554         46,851
          Max Wilhelm       8,297,824         46,581

     and the following persons are incumbent directors whose terms of office 
     continued after the Annual Meeting:

                              Joseph A. Mollica
                              Gary E. Costley
                              W. Clark Still
                              Samuel D. Colella
                              Eileen M. More

(c)  The other matters voted upon and the results of the voting were as follows:

     (1)  The stockholders voted 7,924,605 shares for and 401,651 shares against
          the proposal to approve an amendment to the Company's 1994 Incentive
          Stock Plan to increase the number of shares of Common Stock received
          for issuance by 500,000 shares. Stockholders holding an aggregate of
          18,149 shares abstained from voting on this matter.

                                     -10-
<PAGE>
 
(2)  The stockholders voted 8,335,362 shares for and 6,418 shares against the
     proposal to confirm the appointment of Ernst & Young, LLP as independent
     auditors for the 1997 fiscal year. Stockholders holding an aggregate of
     2,625 shares abstained from voting on this matter.

(3)  A separate tabulation of the votes cast for each director are set forth 
     under Item 4(b) above.

There were no broker non-votes on the forgoing matters.

                                     -11-
<PAGE>
 
     ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K

(a)  Exhibits:

3.1******           Restated Certificate of Incorporation of the Registrant.
3.3******           Bylaws of the Registrant, as amended.
4.3*                Stockholders Rights Agreement, dated February 15, 1995.
10.1*               Series A and Series B Preferred Stock Purchase Agreement, 
                    dated July 21, 1993.
10.2*               Series B Preferred Stock Purchase Agreement, dated March 11,
                    1994.
10.3*               Series C Preferred Stock Purchase Agreement, dated December 
                    22, 1994.
10.4*               Series D Preferred Stock Purchase Agreement, dated February 
                    15, 1995.
10.5**diamond       Amended 1994 Incentive Stock Plan.
10.5(a)diamond      Amended No. 3 to the 1994 Incentive Stock Plan dated May 9, 
                    1997.
10.6*diamond        1995 Employee Stock Purchase Plan.
10.7*diamond        1995 Director Option Plan.
10.8*+              Library Collection Agreement, dated as of October 1, 1995, 
                    between Pharmacopeia and Sandoz Pharma Ltd.
10.9*+              Research, License, and Royalty Agreement, dated as of
                    February 15, 1995, between Pharmacopeia and Berlex
                    Laboratories, Inc.
10.9(a)++           Amendment No. 1 to Research, License and Royalty Agreement
                    between the Company and Berlex Laboratories, Inc. dated
                    November 27, 1996.
10.9(b)++           Amendment No. 2 to Research, License and Royalty Agreement
                    between the Company and Berlex Laboratories, Inc. dated
                    June 30, 1997.
10.10*+             License Agreement, dated as of October 6, 1995, among
                    Pharmacopeia, the Trustees of Columbia University in the
                    City of New York and Cold Spring Harbor Laboratory.
10.11*+             Collaboration Agreement, dated as of December 22, 1994,
                    between Pharmacopeia and Schering Corporation and Schering-
                    Plough, Ltd.
10.11(b)++          Amendment No. 2 to Collaboration Agreement and Random
                    Library Agreement between the Company and Schering
                    Corporation and Schering-Plough, Ltd. dated as of April 22,
                    1996.
10.11(c)++          Amendment No. 3 to Collaboration Agreement and Random
                    Library Agreement between the Company and Schering
                    Corporation and Schering-Plough, Ltd. dated as of April 21,
                    1997.
10.12*+             Random Library Agreement, dated as of December 22, 1994,
                    between Pharmacopeia and Schering Corporation and Schering-
                    Plough, Ltd.
10.13*              Lease Agreement between Pharmacopeia and Eastpark at 8A.
10.13(a)**          Amendment dated as of January 22, 1996 to Lease Agreement 
                    between Pharmacopeia and Eastpark at 8A.
10.13(b)****        Third Amendment to Lease Agreement dated March 31, 1996 
                    between Pharmacopeia and Eastpark at 8A.
10.14*              Sublease, dated as of December 7, 1994, between Pharmacopeia
                    and Enichem Americas, Inc.
10.15*              Lease, dated as of May 2, 1994, between Pharmacopeia and 
                    College Road Associates Limited, as amended.
10.15(a)**          Lease, dated as of December 1, 1995, between Pharmacopeia
                    and College Road Associates, as amended.
10.15(b)****        Third Execution and Modification of lease dated June 7,
                    1996, between Pharmacopeia and College Road Associates
                    Limited.

                                     -12-
<PAGE>
 
10.17*diamond       Employment Agreement, dated October 4, 1994, between the 
                    Company and Lewis J. Shuster.
10.18*diamond       Employment Agreement, dated January 18, 1994, between the 
                    Company and Joseph A. Mollica, Ph.D.
10.19*diamond       Employment Agreement, dated May 18, 1993, between the 
                    Company and John C. Chabala, Ph.D.
10.20*diamond       Employment Agreement, dated June 3, 1993, between the 
                    Company and John J. Baldwin, Ph.D.
10.21*diamond       Employment Agreement, dated December 2, 1993, between the 
                    Company and Nolan H. Sigal, M.D., Ph.D.
10.22*diamond       Consulting Agreement, dated April 30, 1993, between the 
                    Company and W. Clark Still, Ph.D.
10.23*              Warrant to purchase Common Stock issued to Columbia 
                    University.
10.24*              Warrant to purchase Common Stock issued to Cold Spring 
                    Harbor Laboratory.
10.25**+            Collaboration Agreement effective as of December 31, 1995 
                    between Pharmacopeia and Bayer 
10.26**+            Random Library Agreement effective as of December 31, 1995 
                    between Pharmacopeia and Bayer
10.29**diamond      Employment Agreement, dated January 24, 1996, between the 
                    Company and Nancy M. Gray, Ph.D.
10.30***+           Collaborative Agreement dated as of March 29, 1996 with 
                    Daiichi Pharmaceutical Co., Ltd.
10.30(a)++          Amendment No. 1 to Collaboration Agreement between the
                    Company and Daiichi Pharmaceutical Co. Ltd, dated April 14,
                    1997.
10.31****+          Research Agreement, between Pharmacopeia, Inc. and N.V. 
                    Organon dated May 31, 1996
10.32*****diamond   Employment Agreement, dated June 20, 1996, between the 
                    Company and Stephen A. Spearman, Ph.D.
10.33*****          Lease Agreement, dated June 21, 1996, between Pharmacopeia 
                    and South Brunswick Rental I, Ltd.
11.1*               Statement re Computation of Per Share Earnings.
27.1                Financial Data Schedule
27.2                Amended Financial Data Schedule

_______________________

*Incorporated by reference to the same numbered exhibit filed with the Company's
Registration Statement on Form S-1 No. 33-93460.
**Incorporated by reference to the same numbered exhibit filed with the 
Company's Form 10-K for the year ended December 31, 1995.
***Incorporated by reference to the same numbered exhibit filed with the 
Company's Form 10-Q for the quarter ended March 31, 1996.
****Incorporated by reference to the same numbered exhibit filed with the 
Company's Form 10-Q for the quarter ended June 30, 1996.
*****Incorporated by reference to the same numbered exhibit filed with the 
Company's Form 10-Q for the quarter ended September 30, 1996.
******Incorporated by reference to the same numbered exhibit filed with the 
Company's Form 10-K for the year ended December 31, 1996.
+Confidential treatment granted.
++Confidential treatment requested.
(Diamond) Represents a management contract or compensatory plan or arrangement.

(b)  Reports on Form 8-K

          None

                                     -13-
<PAGE>
 
                                  SIGNATURES


     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, thereunto duly authorized.


                                     PHARMACOPEIA, INC.


                                     By: /s/ LEWIS J. SHUSTER
                                         -------------------------------


                                         Lewis J. Shuster
                                         Executive Vice President, Corporate   
                                         Development & Chief Financial Officer
                                         (Duly Authorized Officer and Chief   
                                            Accounting Officer)                 


                                     Date:  August 12, 1997
   
                                     -14-
<PAGE>
 
                              PHARMACOPEIA, INC.
                               INDEX TO EXHIBITS


EXHIBIT NUMBER EXHIBIT NAME                                                 PAGE

     10.5 (a)  Amendment No. 3 to the 1994 Incentive Stock Plan dated May 9, 
               1997.
            
     10.9 (a)  Amendment No. 1 to Research, License and Royalty Agreement
               between the Company and Berlex Laboratories, Inc. dated November
               27, 1996.
            
     10.9 (b)  Amendment No. 2 to Research, License and Royalty Agreement
               between the Company and Berlex Laboratories, Inc. dated June 30,
               1997.

     10.11(b)  Amendment No.2 to Collaboration Agreement and Random Library
               Agreement between the Company and Schering Corporation and
               Schering-Plough, Ltd. dated as of April 22, 1996.

     10.11(c)  Amendment No. 3 to Collaboration Agreement and Random Library
               Agreement between the Company and Schering Corporation and
               Schering-Plough, Ltd. dated as of April 21, 1997.

     10.30(a)  Amendment No.1 to Collaboration Agreement between the Company and
               Daiichi Pharmaceutical Co., Ltd. dated April 14, 1997.

      27.1     Financial Data Schedule

                                     -15-