SECURITIES AND EXCHANGE COMMISSION
Washington, DC 20549

SCHEDULE 13G/A
(Rule 13d-102)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT
TO RULES 13d-1(b) (c) AND (d) AND AMENDMENTS THERETO FILED
PURSUANT TO 13d-2(b)
(Amendment No. 3)1

    ArQule, Inc.
(Name of Issuer)		    

 
 
 
 
 
    Common Stock
(Title of Class of Securities)		    

 
 
 
 
 
    04269E 10 7
(CUSIP Number)		    

 
 
 
 
 
    December 31, 2004
(Date of Event Which Requires Filing of this Statement)		    

Check the appropriate box to designate the rule pursuant to which this Schedule is filed:

    o Rule 13d-1(b)
ý Rule 13d-1(c)
o Rule 13d-1(d)

1        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 disclosures provided in a prior cover page.

         The information required on 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 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).

     
CUSIP No. 04269E 10 7   13G   Page 2 of 10 Pages
     
1   NAME OF REPORTING PERSON:
 Biotechnology Value Fund, L.P.
I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY):		    
2   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*   (a)  ý
        (b)  o
         
3   SEC USE ONLY    

 
 
 
 
 
4   CITIZENSHIP OR PLACE OF ORGANIZATION

 
 
Delaware
 
 
    5   SOLE VOTING POWER
NUMBER OF       0
SHARES  
BENEFICIALLY   6   SHARED VOTING POWER
OWNED       811,532
BY  
EACH   7   SOLE DISPOSITIVE POWER
REPORTING       0
PERSON  
WITH:   8   SHARED DISPOSITIVE POWER
        811,532
9   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON    

 
 
811,532
 
 
10   CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*   o

 
 
 
 
 
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)    

 
 
2.81%
 
 
12   TYPE OF REPORTING PERSON*    

 
 
PN
 
 

*SEE INSTRUCTIONS BEFORE FILLING OUT!

      
CUSIP No. 04269E 10 7   13G   Page 3 of 10 Pages
     
1   NAME OF REPORTING PERSON:
 Biotechnology Value Fund II, L.P.
I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY):		    
2   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*   (a)  ý
        (b)  o
         
3   SEC USE ONLY    

 
 
 
 
 
4   CITIZENSHIP OR PLACE OF ORGANIZATION    

 
 
Delaware
 
 
    5   SOLE VOTING POWER
NUMBER OF       0
SHARES  
BENEFICIALLY   6   SHARED VOTING POWER
OWNED       560,000
BY  
EACH   7   SOLE DISPOSITIVE POWER
REPORTING       0
PERSON  
WITH:   8   SHARED DISPOSITIVE POWER
        560,000
9   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON    

 
 
560,000
 
 
10   CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*   o

 
 
 
 
 
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)    

 
 
1.94%
 
 
12   TYPE OF REPORTING PERSON*    

 
 
PN
 
 

*SEE INSTRUCTIONS BEFORE FILLING OUT!

      
CUSIP No. 04269E 10 7   13G   Page 4 of 10 Pages
     
1   NAME OF REPORTING PERSON:
 BVF Investments, L.L.C.
I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY):		    
2   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*   (a)  ý
        (b)  o
         
3   SEC USE ONLY    

 
 
 
 
 
4   CITIZENSHIP OR PLACE OF ORGANIZATION    

 
 
Delaware
 
 
    5   SOLE VOTING POWER
NUMBER OF       0
SHARES  
BENEFICIALLY   6   SHARED VOTING POWER
OWNED       1,316,800
BY  
EACH   7   SOLE DISPOSITIVE POWER
REPORTING       0
PERSON  
WITH:   8   SHARED DISPOSITIVE POWER
        1,316,800
9   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON    

 
 
1,316,800
 
 
10   CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*   o

 
 
 
 
 
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)    

 
 
4.56%
 
 
12   TYPE OF REPORTING PERSON*    

 
 
OO
 
 

*SEE INSTRUCTIONS BEFORE FILLING OUT!

      
CUSIP No. 04269E 10 7   13G   Page 5 of 10 Pages
     
1   NAME OF REPORTING PERSON:
 Investment 10, L.L.C.
I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY):		    
2   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*   (a)  ý
        (b)  o
         
3   SEC USE ONLY    

 
 
 
 
 
4   CITIZENSHIP OR PLACE OF ORGANIZATION    

 
 
Illinois
 
 
    5   SOLE VOTING POWER
NUMBER OF       0
SHARES  
BENEFICIALLY   6   SHARED VOTING POWER
OWNED       171,000
BY  
EACH   7   SOLE DISPOSITIVE POWER
REPORTING       0
PERSON  
WITH:   8   SHARED DISPOSITIVE POWER
        171,000
9   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON    

 
 
171,000
 
 
10   CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*   o

 
 
 
 
 
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)    

 
 
0.59%
 
 
12   TYPE OF REPORTING PERSON*    

 
 
OO
 
 

*SEE INSTRUCTIONS BEFORE FILLING OUT!

      
CUSIP No. 04269E 10 7   13G   Page 6 of 10 Pages
     
1   NAME OF REPORTING PERSON:
 BVF Partners L.P.
I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY):		    
2   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*   (a)  ý
        (b)  o
         
3   SEC USE ONLY    

 
 
 
 
 
4   CITIZENSHIP OR PLACE OF ORGANIZATION    

 
 
Delaware
 
 
    5   SOLE VOTING POWER
NUMBER OF       0
SHARES  
BENEFICIALLY   6   SHARED VOTING POWER
OWNED       2,859,332
BY  
EACH   7   SOLE DISPOSITIVE POWER
REPORTING       0
PERSON  
WITH:   8   SHARED DISPOSITIVE POWER
        2,859,332
9   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON    

 
 
2,859,332
 
 
10   CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*   o

 
 
 
 
 
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)    

 
 
9.90%
 
 
12   TYPE OF REPORTING PERSON*    

 
 
PN
 
 

*SEE INSTRUCTIONS BEFORE FILLING OUT!

      
CUSIP No. 04269E 10 7   13G   Page 7 of 10 Pages
     
1   NAME OF REPORTING PERSON:
 BVF Inc.
S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY):		    
2   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*   (a)  ý
        (b)  o
         
3   SEC USE ONLY    

 
 
 
 
 
4   CITIZENSHIP OR PLACE OF ORGANIZATION    

 
 
Delaware
 
 
    5   SOLE VOTING POWER
NUMBER OF       0
SHARES  
BENEFICIALLY   6   SHARED VOTING POWER
OWNED       2,859,332
BY  
EACH   7   SOLE DISPOSITIVE POWER
REPORTING       0
PERSON  
WITH:   8   SHARED DISPOSITIVE POWER
        2,859,332
9   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON    

 
 
2,859,332
 
 
10   CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*   o

 
 
 
 
 
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)    

 
 
9.90%
 
 
12   TYPE OF REPORTING PERSON*    

 
 
IA, CO
 
 

*SEE INSTRUCTIONS BEFORE FILLING OUT!

      
CUSIP No. 04269E 10 7   13G   Page 8 of 10 Pages
     

ITEM 1(a).      NAME OF ISSUER:

                        ArQule, Inc. ("ArQule")

ITEM 1(b).      ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES:

                        19 Presidential Way
                         Woburn, Massachusetts 01801-5140

ITEM 2(a).      NAME OF PERSON FILING:

                        This Amendment to Schedule 13G is being filed on behalf of the following persons (the "Reporting Persons"):

  (i)   Biotechnology Value Fund, L.P. ("BVF")
  (ii)   Biotechnology Value Fund II, L.P. ("BVF2")
  (iii)   BVF Investments, L.L.C. ("Investments")
  (iv)   Investment 10, L.L.C. ("ILL10")
  (v)   BVF Partners L.P. ("Partners")
  (vi)   BVF Inc. ("BVF Inc.")

ITEM 2(b).      ADDRESS OF PRINCIPAL BUSINESS OFFICE:

                        The principal business office of the Reporting Persons comprising the group filing this Amendment to Schedule 13G is located at 227 West Monroe Street, Suite 4800, Chicago, Illinois, 60606.

ITEM 2(c).      CITIZENSHIP:

    BVF: a Delaware limited partnership
    BVF2: a Delaware limited partnership
    Investments: a Delaware limited liability company
    ILL10: an Illinois limited liability company
    Partners: a Delaware limited partnership
    BVF Inc.: a Delaware corporation

ITEM 2(d).      TITLE OF CLASS OF SECURITIES:

                        This Amendment to Schedule 13G is being filed with respect to the common stock, par value $0.01 per share (the "Common Stock"), of ArQule. The Reporting Persons' percentage ownership of Common Stock is based on 28,894,906 shares of Common Stock being outstanding.

ITEM 2(e).      CUSIP Number:

                        04269E 10 7

      
CUSIP No. 04269E 10 7   13G   Page 9 of 10 Pages
     

ITEM 3.        IF THIS STATEMENT IS FILED PURSUANT TO RULE 13d-1(b), or 13d-2(b) or (c) CHECK WHETHER THE PERSON FILING IS:    One of the following

                        Not applicable as this Amendment to Schedule 13G is filed pursuant to Rule 13d-1(c).

ITEM 4.        OWNERSHIP:

                        The information in items 1 and 5 through 11 on the cover pages (pp. 2 - 7) on this Amendment to Schedule 13G is hereby incorporated by reference.

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 Persons have ceased to be the beneficial owner of more than five percent of the class of securities check the following.  o

ITEM 6.        OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER PERSON:

                        Pursuant to the operating agreement of Investments, Partners is authorized, among other things, to invest the funds of Ziff Asset Management, L.P., the majority member of Investments, in shares of the Common Stock beneficially owned by Investments and to vote and exercise dispositive power over those shares of the Common Stock. Partners and BVF Inc. share voting and dispositive power over shares of the Common Stock beneficially owned by BVF, BVF2, Investments and those owned by ILL10, on whose behalf Partners acts as an investment manager and, accordingly, Partners and BVF Inc. have beneficial ownership of all of the shares of the Common Stock owned by such parties.

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 A GROUP:

                        Not applicable.

ITEM 9.        NOTICE OF DISSOLUTION OF GROUP:

                        Not applicable.

      
CUSIP No. 04269E 10 7   13G   Page 10 of 10 Pages
     

ITEM 10.        CERTIFICATION

                        By signing below I certify that, to the best of my knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect.

                        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 11, 2005

 
 
BIOTECHNOLOGY VALUE FUND, L.P.

 
 
By:
 
BVF Partners L.P., its general partner

 
 
 
 
By:
 
BVF Inc., its general partner

 
 
 
 
 
 
By:
 
/s/  MARK N. LAMPERT      
               
Mark N. Lampert
President

 
 
BIOTECHNOLOGY VALUE FUND II, L.P.

 
 
By:
 
BVF Partners L.P., its general partner

 
 
 
 
By:
 
BVF Inc., its general partner

 
 
 
 
 
 
By:
 
/s/  MARK N. LAMPERT      
               
Mark N. Lampert
President

 
 
BVF INVESTMENTS, L.L.C.

 
 
By:
 
BVF Partners L.P., its manager

 
 
 
 
By:
 
BVF Inc., its general partner

 
 
 
 
 
 
By:
 
/s/  MARK N. LAMPERT      
               
Mark N. Lampert
President

 
 
INVESTMENT 10, L.L.C.

 
 
By:
 
BVF Partners L.P., its attorney-in-fact

 
 
 
 
By:
 
BVF Inc., its general partner

 
 
 
 
 
 
By:
 
/s/  MARK N. LAMPERT      
               
Mark N. Lampert
President

 
 
BVF PARTNERS L.P.

 
 
By:
 
BVF Partners, L.P., its general partner

 
 
 
 
 
 
By:
 
/s/  MARK N. LAMPERT      
               
Mark N. Lampert
President

 
 
BVF INC.

 
 
 
 
 
 
By:
 
/s/  MARK N. LAMPERT      
               
Mark N. Lampert
President