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                                 UNITED STATES
                      SECURITIES AND EXCHANGE COMMISSION
                            Washington, D.C. 20549

                              Amendment No. 1 to

                                   FORM 10-K

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

                  For the fiscal year ended December 31, 2001

                                      OR

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

            For the transition period from __________to __________

                       Commission file number 000-30992

                      3-DIMENSIONAL PHARMACEUTICALS, INC.
            (Exact name of registrant as specified in its charter)

               Delaware                              23-2716487
       (State of incorporation)         (I.R.S. Employer Identification No.)


Three Lower Makefield Corporate Center, Suite 300, 1020 Stony Hill Road,
Yardley, PA 19067
               (Address of principal offices including zip code)

                                (267) 757-7200
              (Registrant's telephone number including area code)

          SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT:

                                     None

          SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT:

                                     None

  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 for 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 by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained, to
the best of registrant's knowledge, in the definitive proxy statement
incorporated by reference in Part III of this annual report on Form 10-K or
any amendment to this annual report on Form 10-K. [X]

   As of February 11, 2002, the aggregate market value of the Common Stock
held by non-affiliates of the registrant was $111,835,628. Such aggregate
market value was computed by reference to the closing sale price of the Common
Stock as reported on the Nasdaq National Market on such date.

  As of February 11, 2002, there were 22,494,902 shares of the registrant's
Common Stock outstanding.

                      DOCUMENTS INCORPORATED BY REFERENCE

  Portions of the definitive Proxy Statement for the Registrant's 2002 Annual
Meeting of Stockholders to be held on May 17, 2002, to be filed within 120
days after the end of the fiscal year covered by this Annual Report on Form
10-K, are incorporated by reference into Part III of this Report and certain
exhibits are incorporated by reference into Part IV of this Report.

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<TABLE>
<CAPTION>
 Exhibit
 Number                                Description
 -------                               -----------
 <C>     <S>
  10.39  First Amendment to Lease between the Company and Eagleview Technology
         Partners dated October 24, 2000 (incorporated by reference to Exhibit
         10.39 to the Company's Annual Report on Form 10-K (File No. 000-
         30992))./2/
  10.40  Agreement of Sublease between the Company and Advanced Medicine, Inc.,
         dated December 13, 2000 (incorporated by reference to Exhibit 10.40 to
         the Company's Annual Report on Form 10-K (File No. 000-30992))./2/
  10.41  Additional and Alternative Target Agreement between the Company and
         Boehringer Ingelheim Pharmaceuticals, Inc. dated April 20, 2001
         (incorporated by reference to Exhibit 10.41 to the Company's Quarterly
         Report on Form 10-Q for the fiscal quarter period ended June 30, 2001
         (File No. 000-30992))./2/
  10.42  Amendment No. 1 dated May 16, 2001, to Discoverworks Drug Discovery
         Collaboration Agreement between the Company and Bristol-Myers Squibb
         Company, dated July 7, 2000 (incorporated by reference to Exhibit
         10.42 to the Company's Quarterly Report on Form 10-Q for the fiscal
         quarter period ended June 30, 2001 (File No. 000-30992))./2/
  10.43  Agreement of Lease dated June 14, 2001, between the Company and Cedar
         Brook Corporate Center, L.P. (incorporated by reference to Exhibit
         10.43 to the Company's Quarterly Report on Form 10-Q for the fiscal
         quarter period ended June 30, 2001 (File No. 000-30992)).
  10.44  Amendment No. 2 dated October 4, 2001, to Research, Development and
         Commercialization Agreement between the Company and Centocor, Inc.,
         dated December 29, 2000 (incorporated by reference to Exhibit 10.44 to
         the Company's Quarterly Report on Form 10-Q for the fiscal quarter
         period ended September 30, 2001 (File No. 000-30992))./2/
  10.45  Agreement of Lease dated August 8, 2002, between the Company and
         Newtown Office Development III, L.P. (incorporated by reference to
         Exhibit 10.45 to the Company's Quarterly Report on Form 10-Q for the
         fiscal quarter period ended September 30, 2001 (File No. 000-30992)).
  10.46  Collaboration Research and Development Agreement dated October 25,
         2001 between the Company and Athersys, Inc./4/,/5/.
  10.47  Discoverworks Drug Discovery Collaboration Agreement dated December
         28, 2001 between the Company and Janssen Pharmaceuticals and the R.W.
         Johnson Pharmaceutical Research Institute/4/,/5/.
  10.48  License Agreement dated January 7, 2002 between the Company and
         GlaxoSmithKline plc, including Exhibit D consisting of a Stock
         Purchase Agreement and a Registration Rights Agreement between the
         Company and GlaxoSmithKline plc./4/,/5/.
  11.1   Statements or computation of per share income (loss)./5/
  21.1   Subsidiaries of the Registrant (incorporated by reference to the
         Company's Annual Report on Form 10-K (File No. 000-30992)).
  23.1   Consent of Arthur Andersen LLP./5/
  23.2   Consent of Richard A. Eisner & Company, LLP./5/
  99.1   Letter relating to Arthur Andersen LLP./3/
</TABLE>

--------
/1/Compensation plans or arrangements in which directors and executive
   officers are eligible to participate.
/2/Confidential treatment granted with respect to portions of this exhibit.
   Omitted portions were filed separately with the Securities and Exchange
   Commission.
/3/Filed herewith.
/4/Confidential treatment has been requested with respect to portions of this
   exhibit. Omitted portions have been filed separately with the Securities
   and Exchange Commission.
/5/Previously filed.

     (b)  Reports on Form 8-K:

     None

                                     F-26
<PAGE>

                                  SIGNATURES

  Pursuant to the requirements of Section 13 or 15(d) 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.


Date: March 29, 2002                      3-Dimensional Pharmaceuticals, Inc.

                                                  /s/ David C. U'Prichard
                                          By: _________________________________
                                             David C. U'Prichard, Ph.D. Chief
                                              Executive Officer and Director

<TABLE>
<CAPTION>
           Name                            Title                    Date
           ----                            -----                    ----
<S>                                   <C>                     <C>
     /s/ David C. U'Prichard           Chief Executive          March 29, 2002
-------------------------------------   Officer and
     David C. U'Prichard, Ph.D.         Director (Principal
                                        Executive Officer)

         /s/ John M. Gill              Chief Operating          March 29, 2002
-------------------------------------   Officer and
            John M. Gill                Director (Principal
                                        Financial Officer)

       /s/ Scott M. Horvitz            Vice President,          March 29, 2002
-------------------------------------   Finance and
          Scott M. Horvitz              Administration
                                        (Principal
                                        Accounting Officer)

      /s/ F. Raymond Salemme           President, Chief         March 29, 2002
-------------------------------------   Scientific Officer
      F. Raymond Salemme, Ph.D.         and Director

      /s/ James H. Cavanaugh           Director                 March 29, 2002
-------------------------------------
-------------------------------------
      James H. Cavanaugh, Ph.D.
      James H. Cavanaugh, Ph.D.

    /s/ William Claypool. M.D.         Director                 March 29, 2002
-------------------------------------
-------------------------------------
       William Claypool, M.D.

       /s/ Zola P. Horovitz            Director                 March 29, 2002
-------------------------------------
-------------------------------------
       Zola P. Horovitz, Ph.D

        /s/ David R. King              Director                 March 29, 2002
-------------------------------------
-------------------------------------
            David R. King

         /s/ Joshua Ruch               Director                 March 29, 2002
-------------------------------------
-------------------------------------
             Joshua Ruch

       /s/ Harold R. Werner            Director                 March 29, 2002
-------------------------------------
-------------------------------------
          Harold R. Werner
</TABLE>
<PAGE>

<TABLE>
<CAPTION>
 Exhibit
 Number                                Description
 -------                               -----------
 <C>     <S>
  10.43  Agreement of Lease dated June 14, 2001, between the Company and Cedar
         Brook Corporate Center, L.P. (incorporated by reference to Exhibit
         10.43 to the Company's Quarterly Report on Form 10-Q for the fiscal
         quarter period ended June 30, 2001 (File No. 000-30992)).
  10.44  Amendment No. 2 dated October 4, 2001, to Research, Development and
         Commercialization Agreement between the Company and Centocor, Inc.,
         dated December 29, 2000 (incorporated by reference to Exhibit 10.44 to
         the Company's Quarterly Report on Form 10-Q for the fiscal quarter
         period ended September 30, 2001 (File No. 000-30992))./2/
  10.45  Agreement of Lease dated August 8, 2002, between the Company and
         Newtown Office Development III, L.P. (incorporated by reference to
         Exhibit 10.45 to the Company's Quarterly Report on Form 10-Q for the
         fiscal quarter period ended September 30, 2001 (File No. 000-30992)).
  10.46  Collaboration Research and Development Agreement dated October 25,
         2001 between the Company and Athersys, Inc./4/,/5/.
  10.47  Discoverworks Drug Discovery Collaboration Agreement dated December
         28, 2001 between the Company and Janssen Pharmaceuticals and the R.W.
         Johnson Pharmaceutical Research Institute/4/,/5/.
  10.48  License Agreement dated January 7, 2002 between the Company and
         GlaxoSmithKline plc, including Exhibit D consisting of a Stock
         Purchase Agreement and a Registration Rights Agreement between the
         Company and GlaxoSmithKline plc./4/,/5/.
  11.1   Statements or computation of per share income (loss)./5/
  21.1   Subsidiaries of the Registrant (incorporated by reference to the
         Company's Annual Report on Form 10-K (File No. 000-30992)).
  23.1   Consent of Arthur Andersen LLP./5/
  23.2   Consent of Richard A. Eisner & Company, LLP./5/
  99.1   Letter relating to Arthur Andersen LLP./3/
</TABLE>

--------
/1/Compensation plans or arrangements in which directors and executive
   officers are eligible to participate.
/2/Confidential treatment granted with respect to portions of this exhibit.
   Omitted portions were filed separately with the Securities and Exchange
   Commission.
/3/Filed herewith.
/4/Confidential treatment has been requested with respect to portions of this
   exhibit. Omitted portions have been filed separately with the Securities
   and Exchange Commission.
/5/ Previously filed.