SC 13G/A 1 d02-35867.txt AMENDMENT NO. 1 TO SCHEDULE 13G SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13D-1 (b) AND (c) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2(b) (Amendment No. 1)* 3-DIMENSIONAL PHARMACEUTICALS, INC. -------------------------------------------------------------------------------- (Name of Issuer) Common Stock, $.001 par value -------------------------------------------------------------------------------- (Title of Class of Securities) 88554W104 -------------------------------------------------------------------------------- (CUSIP Number) December 31, 2001 -------------------------------------------------------------------------------- Date of Event Which Requires Filing of this Statement Check the appropriate box to designate the rule pursuant to which this Schedule is filed: |_| Rule 13d-1(b) |_| Rule 13d-1(c) |X| Rule 13d-1(d) * The remainder of this cover page shall be filled out for a reporting person's initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter the disclosures provided in a prior cover page. The information required in the remainder of this cover page shall not be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange Act of 1934 ("Act") or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes). (Continued on following page(s)) Page 1 of 24 Pages CUSIP No. 88554W104 13G Page 2 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON HealthCare Ventures III, L.P. -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION Delaware -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 3,182,313 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 3,182,313 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 3,182,313 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 14.47% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 3 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON HealthCare Partners III, L.P. -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION Delaware -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 3,182,313 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 3,182,313 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 3,182,313 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 14.47% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 4 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON HealthCare Ventures IV, L.P. -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION Delaware -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 934,522 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 934,522 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 934,522 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 4.25% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 5 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON HealthCare Partners IV, L.P. -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION Delaware -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 934,522 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 934,522 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 934,522 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 4.25% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 6 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON HealthCare Ventures V, L.P. -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION Delaware -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 365,090 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 365,090 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 365,090 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 1.66% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 7 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON HealthCare Partners V, L.P. -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION Delaware -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 365,090 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 365,090 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 365,090 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 1.66% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 8 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON HealthCare Ventures VI, L.P. -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION Delaware -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 819,595 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 819,595 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 819,595 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 3.73% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 9 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON HealthCare Partners VI, L.P. -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION Delaware -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 819,595 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 819,595 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 819,595 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 3.73% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* PN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 10 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON James H. Cavanaugh, Ph.D. -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION United States -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 5,301,520 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 5,301,520 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 5,301,520 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 24.11% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* IN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 11 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Harold R. Werner -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION United States -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 5,301,520 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 5,301,520 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 5,301,520 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 24.11% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* IN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 12 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON William Crouse -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION United States -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 5,301,520 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 5,301,520 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 5,301,520 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 24.11% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* IN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 13 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON John W. Littlechild -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION United States -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 5,301,520 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 5,301,520 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 5,301,520 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 24.11% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* IN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 14 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Christopher Mirabelli, Ph.D. -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION United States -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 1,184,685 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 1,184,685 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 1,184,685 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 5.39% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* IN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 15 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Augustine Lawlor -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION United States -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 1,184,685 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 1,184,685 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 1,184,685 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 5.39% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* IN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! CUSIP No. 88554W104 13G Page 16 of 24 Pages -------------------------------------------------------------------------------- 1 NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Eric Aguiar, Ph.D. -------------------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| -------------------------------------------------------------------------------- 3 SEC USE ONLY -------------------------------------------------------------------------------- 4 CITIZENSHIP OR PLACE OF ORGANIZATION United States -------------------------------------------------------------------------------- 5 SOLE VOTING POWER -------------------------------------------------------------- NUMBER OF 6 SHARED VOTING POWER SHARES BENEFICIALLY 819,595 OWNED BY -------------------------------------------------------------- EACH 7 SOLE DISPOSITIVE POWER REPORTING PERSON WITH -------------------------------------------------------------- 8 SHARED DISPOSITIVE POWER 819,595 -------------------------------------------------------------------------------- 9 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 819,595 -------------------------------------------------------------------------------- 10 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* |_| -------------------------------------------------------------------------------- 11 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 3.73% -------------------------------------------------------------------------------- 12 TYPE OF REPORTING PERSON* IN -------------------------------------------------------------------------------- *SEE INSTRUCTIONS BEFORE FILLING OUT! Page 17 of 24 pages Item 1. (a) Name of Issuer: 3-Dimensional Pharmaceuticals, Inc. (b) Address of Issuer's Principal Executive Offices: 1020 Stony Hill Road Yardley, Pennsylvania 19067 Item 2. (a) Name of Person Filing: HealthCare Ventures III, L.P. ("HCV III"), HealthCare Partners III, L.P. ("HCP III"), HealthCare Ventures IV, L.P. ("HCV IV"), HealthCare Partners IV, L.P. ("HCP IV"), HealthCare Ventures V, L.P. ("HCV V"), HealthCare Partners V, L.P. ("HCP V"), HealthCare Ventures VI, L.P. ("HCV VI"), HealthCare Partners VI, L.P. ("HCP VI"), Drs. Cavanaugh, Mirabelli and Aguiar and Messrs. Werner, Littlechild, Crouse and Lawlor. See attached Exhibit A, which is a copy of their agreement in writing to file this statement on behalf of each of them.(1) (b) Address of Principal Business Office or, if none, Residence: The business address for HCV III, HCP III, HCV IV, HCP IV, HCV V, HCP V, HCV VI, HCP VI, Drs. Cavanaugh and Aguiar and Messrs. Werner and Crouse is 44 Nassau Street, Princeton, New Jersey 08542. The business address for Dr. Mirabelli and Messrs. Littlechild and Lawlor is One Kendall Square, Building 300, Cambridge, Massachusetts 02339. (c) Citizenship: HCV III, HCP III, HCV IV, HCP IV, HCV V, HCP V, HCV VI and HCP VI are limited partnerships organized under the laws of the State of Delaware. Drs. Cavanaugh, Mirabelli and Aguiar and Messrs. Werner, Littlechild, Crouse and Lawlor are each United States citizens. ---------- (1) Dr. Cavanaugh and Messrs. Werner, Littlechild and Crouse are general partners of HCP III, HCP IV, HCP V and HCP VI, the general partner of each of HCV III, HCV IV, HCV V and VI, respectively, the record holders of Issuer's securities. In addition, Dr. Mirabelli and Mr. Lawlor are also general partners of HCP V and HCP VI, the general partner of each of HCV V and, HCV VI, respectively, the record holders of the Issuer's securities and Dr. Aguiar is a general partner of HCP VI, the general partner of HCV VI, the record holder of the Issuer's securities. Page 18 of 24 pages (d) Title of Class of Securities: Common Stock, par value $.001 (the "Shares"). (e) CUSIP Number: 88554W104 Item 3. If this statement is filed pursuant to Rule 13d-1(b), or 13d-2(b), check whether the person filing is a: Inapplicable. Item 4. Ownership. (a) Amount Beneficially Owned: As of December 31, 2001: HCV III and HCP III beneficially owned 3,182,313 Shares of the Issuer's Common Stock; HCV IV and HCP IV beneficially owned 934,522 Shares of the Issuer's Common Stock; HCV V and HCP V beneficially owned 365,090 Shares of the Issuer's Common Stock; HCV VI and HCP VI beneficially owned 819,595 Shares of the Issuer's Common Stock; Dr. Cavanaugh and Messrs. Werner, Crouse and Littlechild beneficially owned 5,301,520 Shares of the Issuer's Common Stock(2); Dr. Mirabelli and Mr. Lawlor beneficially owned 1,184,685 Shares of the Issuer's Common Stock; and Dr. Aguiar beneficially owned 819,595 Shares of the Issuer's Common Stock. (b) Percent of Class: As of December 31, 2001: the 3,182,313 Shares beneficially owned by HCV III and HCP III constitute 14.47% of the Shares outstanding; the 934,522 Shares beneficially owned by HCV IV and HCP IV constitute 4.25% of the Shares outstanding; the 365,090 Shares beneficially owned by HCV V and HCP V constitute 1.66% of the Shares outstanding; the 819,595 Shares beneficially owned by HCV VI and HCP VI constitute 3.73% of the Shares outstanding; the 5,301,520 Shares beneficially owned by Dr. Cavanaugh and Messrs. Werner, Crouse and Littlechild constitute 24.11% of the Shares outstanding; the 1,184,685 Shares beneficially owned by Dr. Mirabelli and Mr. Lawlor constitute 5.39% of the Shares outstanding; and the 819,595 Shares beneficially owned by Dr. Aguiar constitute 3.73% of the Shares outstanding. ---------- (2) Please note that in addition to the 5,301,520 Shares of the Issuer's Common Stock beneficially owned by Dr. Cavanaugh, Dr. Cavanaugh has been granted options to purchase 10,000 Shares of the Issuer's Common Stock which become exercisable as to 2,500 Shares per year for 4 years beginning on May 14, 2002. Dr. Cavanaugh is not deemed to beneficially own these Shares at the time of this report. Page 19 of 24 pages (c) Number of shares as to which such person has: (i) sole power to vote or to direct the vote: Inapplicable. (ii) shared power to vote or to direct the vote: HCV III, HCP III, Dr. Cavanaugh and Messrs. Werner, Littlechild and Crouse share the power to vote or direct the vote of those Shares owned by HCV III. HCV IV, HCP IV, Dr. Cavanaugh and Messrs. Werner, Littlechild and Crouse share the power to vote or direct the vote of those Shares owned by HCV IV. HCV V, HCP V, Drs. Cavanaugh and Mirabelli and Messrs. Werner, Littlechild, Crouse, and Lawlor share the power to vote or direct the vote of those Shares owned by HCV V. HCV VI, HCP VI, Drs. Cavanaugh, Mirabelli and Aguiar, and Messrs. Werner, Littlechild, Crouse and Lawlor share the power to vote or direct the vote of those Shares owned by HCV VI. (iii) sole power to dispose or to direct the disposition of: Inapplicable. (iv) shared power to dispose of or to direct the disposition of: HCV III, HCP III, Dr. Cavanaugh and Messrs. Werner, Littlechild and Crouse share the power to dispose of or direct the disposition of those Shares owned by HCV III. HCV IV, HCP IV, Dr. Cavanaugh and Messrs. Werner, Littlechild and Crouse share the power to dispose of or direct the disposition of those Shares owned by HCV IV. HCV V, HCP V, Drs. Cavanaugh and Mirabelli and Messrs. Werner, Littlechild, Crouse, and Lawlor share the power to dispose of or direct the disposition of those Shares owned by HCV V. HCV VI, HCP VI, Drs. Cavanaugh, Mirabelli and Aguiar and Messrs. Werner, Littlechild, Crouse and Lawlor share the power to dispose of or direct the disposition of those Shares owned by HCV VI. Page 20 of 24 pages Item 5. Ownership of Five Percent or less of a Class: Inapplicable. Item 6. Ownership of More than Five Percent on Behalf of Another Person: Inapplicable. Item 7. Identification and Classification of the Subsidiary Which Acquired the Security Being Reported on by the Parent Holding Company: Inapplicable. Item 8. Identification and Classification of Members of the Group: Inapplicable. Item 9. Notice of Dissolution of Group: Inapplicable. Item 10. Certification: Inapplicable. Page 21 of 24 pages SIGNATURES After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct. Dated: February 8, 2002 HealthCare Ventures III, L.P., Princeton, New Jersey by its General Partner, HealthCare Partners III, L.P. By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Partners III, L.P. Princeton, New Jersey By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Ventures IV, L.P., Princeton, New Jersey by its General Partner, HealthCare Partners IV, L.P. By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Partners IV, L.P. Princeton, New Jersey By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Ventures V, L.P., Princeton, New Jersey by its General Partner, HealthCare Partners V, L.P. By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Partners V, L.P. Princeton, New Jersey By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Ventures VI, L.P., Princeton, New Jersey by its General Partner, HealthCare Partners VI, L.P. By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Partners VI, L.P. Princeton, New Jersey By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner
page 22 of 24 pages Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Princeton, New Jersey --------------------------------------- James H. Cavanaugh, Ph.D. Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Princeton, New Jersey --------------------------------------- Harold R. Werner Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Princeton, New Jersey --------------------------------------- William Crouse Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Princeton, New Jersey --------------------------------------- Eric Aguiar, Ph.D. Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Cambridge, Massachusetts --------------------------------------- John W. Littlechild Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Cambridge, Massachusetts --------------------------------------- Christopher Mirabelli, Ph.D. Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Cambridge, Massachusetts --------------------------------------- Augustine Lawlor
Page 23 of 24 pages EXHIBIT A AGREEMENT JOINT FILING OF SCHEDULE 13G The undersigned hereby agree to jointly prepare and file with regulatory authorities a Schedule 13G and any future amendments thereto reporting each of the undersigned's ownership of securities of 3-Dimensional Pharmaceuticals Inc. and hereby affirm that such Schedule 13G is being filed on behalf of each of the undersigned. Dated: February 8, 2002 HealthCare Ventures III, L.P., Princeton, New Jersey by its General Partner, HealthCare Partners III, L.P. By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Partners III, L.P. Princeton, New Jersey By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Ventures IV, L.P., Princeton, New Jersey by its General Partner, HealthCare Partners IV, L.P. By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Partners IV, L.P. Princeton, New Jersey By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Ventures V, L.P., Princeton, New Jersey by its General Partner, HealthCare Partners V, L.P. By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Partners V, L.P. Princeton, New Jersey By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Ventures VI, L.P., Princeton, New Jersey by its General Partner, HealthCare Partners VI, L.P. By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner Dated: February 8, 2002 HealthCare Partners VI, L.P. Princeton, New Jersey By: /s/ Jeffrey Steinberg ------------------------------------------------- Administrative Partner
Page 24 of 24 pages Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Princeton, New Jersey --------------------------------------- James H. Cavanaugh, Ph.D. Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Princeton, New Jersey --------------------------------------- Harold R. Werner Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Princeton, New Jersey --------------------------------------- William Crouse Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Princeton, New Jersey --------------------------------------- Eric Aguiar, Ph.D. Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Cambridge, Massachusetts --------------------------------------- John W. Littlechild Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Cambridge, Massachusetts --------------------------------------- Christopher Mirabelli, Ph.D. Dated: February 8, 2002 By: /s/ Jeffrey Steinberg, Attorney-in-Fact Cambridge, Massachusetts --------------------------------------- Augustine Lawlor