ADVANCED TECHNOLOGY VENTURES III
SC 13G/A, 1999-02-16
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                                 UNITED STATES
                      SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C.  20549


                                 SCHEDULE 13G
                                        
                   Under the Securities Exchange Act of 1934
                           (Amendment No.    1    )*
                                         ---------  
                                        

                       CollaGenex Pharmaceuticals, Inc.
- --------------------------------------------------------------------------------
                               (Name of Issuer)

                         Common Stock, $.01 par value
- --------------------------------------------------------------------------------
                        (Title of Class of Securities)

                                  00019419B1
- --------------------------------------------------------------------------------
                                 (CUSIP Number)


                               December 31, 1998
- --------------------------------------------------------------------------------
            (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).

                               Page 1 of 13 pages
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 00019419B1              13G                    PAGE 2 OF 13 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSON
 1    S.S. or I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
                                                                                
      Advanced Technology Ventures III, L.P.                                   
                          
- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
 2                                                              (a) [_]
                                                                (b) [_]
                                                 
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3
 

- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 4                                 
      Delaware

- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     5                                                       
     NUMBER OF            
                          Under 5%
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      6       
                          
     OWNED BY             Under 5%
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     7       
    REPORTING             
                          Under 5%
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH          8       
                          Under 5%
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 9                           
      Under 5%
- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*
10           
                                                                    [_]
 
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
11           
                                                                         
      Under 5%
- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
12           
      
      PN
- ------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 2 of 13 pages
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 00019419B1              13G                    PAGE 3 OF 13 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSON
 1    S.S. or I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
                                                                                
      ATV Associates III, L.P.                                   
                          
- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
 2                                                              (a) [_]
                                                                (b) [_]
                                                 
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3
 

- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 4                                 
      Delaware

- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     5                                                       
     NUMBER OF            
                          Under 5%
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      6       
                          
     OWNED BY             Under 5%
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     7       
    REPORTING             
                          Under 5%
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH          8       
                          Under 5%
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 9                           
      Under 5%
- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*
10           
                                                                    [_]
 
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
11           
                                                                         
      Under 5%
- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
12           
      
      PN
- ------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 3 of 13 pages
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 00019419B1              13G                    PAGE 4 OF 13 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSON
 1    S.S. or I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
                                                                                
      Albert E. Paladino
                          
- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
 2                                                              (a) [_]
                                                                (b) [_]
                                                 
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3
 

- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 4                                 
      United States

- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     5                                                       
     NUMBER OF            
                          Under 5%
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      6       
                          
     OWNED BY             Under 5%
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     7       
    REPORTING             
                          Under 5%
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH          8       
                          Under 5%
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 9                           
      Under 5%
- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*
10           
                                                                    [_]
 
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
11           
                                                                         
      Under 5%
- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
12           
      
      IN
- ------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 4 of 13 pages
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 00019419B1              13G                    PAGE 5 OF 13 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSON
 1    S.S. or I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
                                                                                
      Pieter J. Schiller
                          
- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
 2                                                              (a) [_]
                                                                (b) [_]
                                                 
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3
 

- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 4                                 
      United States

- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     5                                                       
     NUMBER OF            
                          Under 5%
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      6       
                          
     OWNED BY             Under 5%
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     7       
    REPORTING             
                          Under 5%
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH          8       
                          Under 5%
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 9                           
      Under 5%
- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*
10           
                                                                    [_]
 
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
11           
                                                                         
      Under 5%
- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
12           
      
      IN
- ------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 5 of 13 pages
<PAGE>
 
- -----------------------                                  ---------------------
  CUSIP NO. 00019419B1              13G                    PAGE 6 OF 13 PAGES
- -----------------------                                  ---------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSON
 1    S.S. or I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
                                                                                
      Jos C. Henkens    
                          
- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
 2                                                              (a) [_]
                                                                (b) [_]
                                                 
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3
 

- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 4                                 
      United States

- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     5                                                       
     NUMBER OF            
                          Under 5%
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      6       
                          
     OWNED BY             Under 5%
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     7       
    REPORTING             
                          Under 5%
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH          8       
                          Under 5%
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 9                           
      Under 5%
- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*
10           
                                                                    [_]
 
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
11           
                                                                         
      Under 5%
- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
12           
      
      IN
- ------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 6 of 13 pages
<PAGE>
 
Item 1(a).  Name of Issuer:  CollaGenex Pharmaceuticals, Inc.
            ---------------                                  

Item 1(b).  Address of Issuer's Principal Executive Offices:
            ----------------------------------------------- 
            301 South State Street, Newtown, PA  18940.

Item 2(a).  Names of Persons Filing: Advanced Technology Ventures III, L.P., ATV
            -----------------------                                             
            Associates III, L.P., Albert E. Paladino, Pieter J. Schiller and Jos
            C. Henkens.

            ATV Associates III, L.P. is the sole general partner of Advanced
            Technology Ventures III, L.P. Messrs. Schiller and Henkens are
            individual general partners of ATV Associates III, L.P. Prior to
            December 31, 1998, Mr. Paladino was an individual general partner of
            ATV Associates III, L.P.

Item 2(b).  Address of Principal Business Office or, if None, Residence:
            ----------------------------------------------------------- 

            The address of the principal business office of Advanced Technology
            Ventures III, L.P., ATV Associates III, L.P., Albert E. Paladino and
            Pieter J. Schiller is 281 Winter Street, Waltham, MA 02154. The
            address of the principal business office of Jos C. Henkens is 485
            Ramona Street, Suite 200, Palo Alto, California 94301.

Item 2(c).  Citizenship:  Advanced Technology Ventures III, L.P. and ATV
            -----------                                                 
            Associates III, L.P. are limited partnerships organized under the
            laws of the State of Delaware. Each of Messrs. Paladino, Schiller
            and Henkens is a United States citizen.

Item 2(d).  Title of Class of Securities: Common Stock, $.01 par value per share
            ----------------------------                                        

 
Item 2(e).  CUSIP Number:                     00019419B1
            -------------
 
Item 3.     If this statement if filed pursuant to Rules 13d-1(b), or 13d-2(b) 
            ------------------------------------------------------------------
            or (c), check whether the person filing is a:
            ----------------------------------------------
 
            (a) [  ]   Broker or Dealer registered under Section 15 of the 
                       Securities Exchange Act of 1934 (the "Act").
            (b) [  ]   Bank as defined in Section 3(a)(6) of the Act.
            (c) [  ]   Insurance Company as defined in Section 3(a)(19) of the 
                       Act.
            (d) [  ]   Investment Company registered under Section 8 of the 
                       Investment Company Act of 1940.
            (e) [  ]   An investment adviser in accordance with Rule 13d-1(b)
                       (1)(ii)(E).
            (f) [  ]   An employee benefit plan or endowment fund in 
                       accordance with  Rule 13d-1(b)(1)(ii)(F);
            (g) [  ]   A parent holding company or control person in 
                       accordance with Rule 13d-1(b)(1)(ii)(G).

                               Page 7 of 13 pages
<PAGE>
 
            (h) [  ]   A savings association as defined in Section 3(b) of the 
                       Federal Deposit Insurance Act;
            (i) [  ]   A church plan that is excluded from the definition of 
                       an investment company under Section 3(c)(14) of the 
                       Investment Company Act;
            (j) [  ]   Group, in accordance with Rule 13d-1(c), check this 
                       box [  ].
            Not Applicable.

Item 4.    Ownership.
           --------- 

          (a)  Amount Beneficially Owned:


               Each of Advanced Technology Ventures III, L.P., ATV Associates
               III, L.P., Albert E. Paladino, Pieter J. Schiller and Jos C.
               Henkens may be deemed to own beneficially less than 5% of the
               outstanding shares of Common Stock as of December 31, 1998.

          (b)  Percent of Class:

               Not applicable.

          (c)  Number of shares as to which such person has:

               (i)   sole power to vote or to direct the vote:

                     Advanced Technology Ventures III, L.P.:  Under 5%
                     ATV Associates III, L.P.:  Under 5%
                     Albert E. Paladino:  Under 5%
                     Pieter J. Schiller:  Under 5%
                     Jos C. Henkens:  Under 5%

               (ii)  shared power to vote or to direct the vote:

                     Advanced Technology Ventures III, L.P.:  Under 5%
                     ATV Associates III, L.P.:  Under 5%
                     Albert E. Paladino:  Under 5%
                     Pieter J. Schiller:  Under 5%
                     Jos C. Henkens:  Under 5%

               (iii) sole power to dispose or direct the disposition:

                     Advanced Technology Ventures III, L.P.:  Under 5%
                     ATV Associates III, L.P.:  Under 5%
                     Albert E. Paladino:  Under 5%
                     Pieter J. Schiller:  Under 5%
                     Jos C. Henkens:  Under 5%

               (iv)  shared power to dispose or direct the disposition:

                               Page 8 of 13 pages
<PAGE>
 
                     Advanced Technology Ventures III, L.P.:  Under 5%
                     ATV Associates III, L.P.:  Under 5%
                     Albert E. Paladino:  Under 5%
                     Pieter J. Schiller:  Under 5%
                     Jos C. Henkens:  Under 5%

Item 5.    Ownership of Five Percent or Less of a Class.
           -------------------------------------------- 

           If this statement is being filed to report the fact that as of the
           date hereof the reporting person has ceased to be the beneficial
           owner of more than five percent of the class of securities, check the
           following [ X ].

           Each Reporting Person has ceased to own beneficially more than 5% of
           the outstanding Common Stock of CollaGenex Pharmaceuticals, Inc.

Item 6.    Ownership of More than Five Percent on Behalf of Another Person.
           --------------------------------------------------------------- 

           Not Applicable.

Item 7.    Identification and Classification of the Subsidiary which Acquired 
           ---------------------------------------------------------------------
           the Security Being Reported on By the Parent Holding Company.
           ------------------------------------------------------------- 

           Not Applicable.

Item 8.    Identification and Classification of Members of the Group.
           --------------------------------------------------------- 

           Not Applicable.  The Reporting Persons expressly disclaim membership
           in a "group" within the meaning of Regulation 13D.

Item 9.    Notice of Dissolution of Group.
           ------------------------------ 

           Not Applicable.

Item 10.   Certifications.
           -------------- 

           Not Applicable.  This statement on Schedule 13G is not filed pursuant
           to Rule 13d-1(b) or Rule 13d-1(c).

                               Page 9 of 13 pages
<PAGE>
 
                                   SIGNATURES
                                   ----------
                                        
  After reasonable inquiry and to the best of my knowledge and belief, we
certify that the information set forth in this statement is true, complete and
correct.  We also hereby agree to file this statement jointly pursuant to the
Agreement set forth as Exhibit 1 hereto.

Date:  February 10, 1999


ADVANCED TECHNOLOGY VENTURES III, L.P.

By:  ATV Associates III, L.P.

By:  /s/ Pieter J. Schiller
     ----------------------
     Pieter J. Schiller,
     General Partner


ATV ASSOCIATES III, L.P.

By:  /s/ Pieter J. Schiller
     ----------------------
     Pieter J. Schiller,
     General Partner


/s/ Pieter J. Schiller
- ---------------------------
Pieter J. Schiller


                    *
- ---------------------------
Albert E. Paladino


                    *
- ---------------------------
Jos C. Henkens



                                    *By:   /s/ Pieter J. Schiller
                                          -------------------------------------
                                          Pieter J. Schiller
                                          Attorney-in-Fact

- --------------------------------------------------------------------------------
     This Schedule 13G is executed by Pieter J. Schiller pursuant to an executed
Power of Attorney filed with the Securities and Exchange Commission on February
13, 1998 in connection with a Schedule 13G for RF Micro Devices, Inc., which
Power of Attorney is incorporated herein by reference and copy of which is
attached hereto as Exhibit 2.

                              Page 10 of 13 pages
<PAGE>
 
                                                                       EXHIBIT 1
                                                                       ---------

                                   AGREEMENT
                                   ---------
                                        
  Pursuant to Rule 13d-1(f)(1) under the Securities Exchange Act of 1934, the
undersigned hereby agree that only one statement containing the information
required by Schedule 13G need be filed with respect to the ownership by each of
the undersigned of shares of Common Stock of CollaGenex Pharmaceuticals, Inc.

  This Agreement may be executed in any number of counterparts, each of which
shall be deemed an original.

Date:  February 10, 1999

ADVANCED TECHNOLOGY VENTURES III, L.P.

By:  ATV Associates III, L.P.

By:  /s/ Pieter J. Schiller
     ----------------------
     Pieter J. Schiller,
     General Partner

ATV ASSOCIATES III, L.P.

By:  /s/ Pieter J. Schiller
     ----------------------
     Pieter J. Schiller,
     General Partner

/s/ Pieter J. Schiller
- ---------------------------
Pieter J. Schiller

                      *
- ---------------------------
Albert E. Paladino

                      *
- ---------------------------
Jos C. Henkens


                                    *By:  /s/ Pieter J. Schiller
                                          ------------------------------
                                          Pieter J. Schiller
                                          Attorney-in-Fact
- --------------------------------------------------------------------------------
          This Agreement is executed by Pieter J. Schiller pursuant to an
executed Power of Attorney filed with the Securities and Exchange Commission on
February 13, 1998 in connection with a Schedule 13G for RF Micro Devices, Inc.,
which Power of Attorney is incorporated herein by reference and copy of which is
attached hereto as Exhibit 2.

                              Page 11 of 13 pages
<PAGE>
 
                                                                       EXHIBIT 2
                                                                       ---------
                                                                                

                               POWER OF ATTORNEY


          KNOW ALL MEN BY THESE PRESENTS, that each person whose signature
appears below hereby constitutes and appoints Pieter J. Schiller his true and
lawful attorney-in fact, with full power of substitution, to sign any and all
instruments, certificates and documents that may be necessary, desirable or
appropriate to be executed on behalf of himself as an individual or in his
capacity as a general partner of any partnership, pursuant to Section 13 or 16
of the Securities Exchange Act of 1934, as amended (the "Exchange Act"), and any
and all regulations promulgated thereunder, and to file the same, with all
exhibits thereto, and any other documents in connection therewith, with the
Securities and Exchange Commission, and with any other entity when and if such
is mandated by the Exchange Act or by the By-laws of the National Association of
Securities Dealers, Inc., granting unto said attorney-in-fact full power and
authority to do and perform each and every act and thing necessary, desirable or
appropriate, fully to all intents and purposes as he might or could do in
person, thereby ratifying and confirming all that said attorney-in fact, or his
substitutes, may lawfully do or cause to be done by virtue hereof.

          IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 
12th day of February, 1998.



By:  /s/ Albert E. Paladino
     ----------------------
     Albert E. Paladino

By:  ----------------------
     Jos C. Henkens

                              Page 12 of 13 pages
<PAGE>
 
                                                                       EXHIBIT 2
                                                                       ---------
                                                                                

                               POWER OF ATTORNEY


   KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears
below hereby constitutes and appoints Pieter J. Schiller his true and lawful
attorney-in fact, with full power of substitution, to sign any and all
instruments, certificates and documents that may be necessary, desirable or
appropriate to be executed on behalf of himself as an individual or in his
capacity as a general partner of any partnership, pursuant to Section 13 or 16
of the Securities Exchange Act of 1934, as amended (the "Exchange Act"), and any
and all regulations promulgated thereunder, and to file the same, with all
exhibits thereto, and any other documents in connection therewith, with the
Securities and Exchange Commission, and with any other entity when and if such
is mandated by the Exchange Act or by the By-laws of the National Association of
Securities Dealers, Inc., granting unto said attorney-in-fact full power and
authority to do and perform each and every act and thing necessary, desirable or
appropriate, fully to all intents and purposes as he might or could do in
person, thereby ratifying and confirming all that said attorney-in fact, or his
substitutes, may lawfully do or cause to be done by virtue hereof.

   IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 12th day
of February, 1998.


By:  -------------------
     Albert E. Paladino

By:  /s/ Jos C. Henkens
     -------------------
     Jos C. Henkens

                              Page 13 of 13 pages


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