Exhibit 99.1

    Certification by the Chief Executive Officer and Chief Financial Officer
          Relating to a Periodic Report Containing Financial Statements

         I, David C. U'Prichard, Chief Executive Officer, and I, Scott M.
Horvitz, Chief Financial Officer, of 3-Dimensional Pharmaceuticals, Inc., a
Delaware corporation (the "Company"), each hereby certifies that:

         (1)   The Company's periodic report on Form 10-Q for the period ended
June 30, 2002 (the "Form 10-Q") fully complies with the requirements of Section
13(a) of the Securities Exchange Act of 1934, as amended; and

         (2)   The information contained in the Form 10-Q fairly presents, in
all material respects, the financial condition and results of operations of the
Company.

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CHIEF EXECUTIVE OFFICER                     CHIEF FINANCIAL OFFICER

/s/ David C. U'Prichard                     /s/ Scott M. Horvitz
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David C. U'Prichard                         Scott M. Horvitz

Date: August 9, 2002                        Date: August 9, 2002
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