SECURITIES AND EXCHANGE COMMISSION
Washington, DC 20549

SCHEDULE 13G
(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.____)*

 

Ligand Pharmaceuticals Incorporated

(Name of Issuer)
 

Common Stock

(Title of Class of Securities)

 

53220K207

(CUSIP Number)

 

October 28, 2008

(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)
 

 x

Rule 13d-1(c)
 

o

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 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. 53220K207

 

13G

 

Page 2 of 12 Pages

1

 

NAME OF REPORTING PERSON:
Biotechnology Value Fund, L.P.

 

 
 

2

 

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

 (a)

  x

 

 

 

 (b)

o

 

 

 

 

 
 

3

 

SEC USE ONLY

 

 

 

 

 

 

 
 

4

 

CITIZENSHIP OR PLACE OF ORGANIZATION

 

 

Delaware

 

 

 

 


5

 


SOLE VOTING POWER 

NUMBER OF

SHARES

BENEFICIALLY

OWNED

BY

EACH

REPORTING

PERSON

WITH:

         

 

 

 

0

 

  

 

6

 

SHARED VOTING POWER

 

 

  

2,328,648

 

  

 

7

 

SOLE DISPOSITIVE POWER

 

 

 

0

 

  

 

8

 

SHARED DISPOSITIVE POWER

 

 

 

2,328,648
 

9

 

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

 

 

 

 

2,328,648

 

 
 

10

 

CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*

 

o

 

 

 

 

 
 

11

 

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

 

 

 

 

2.45%

 

 
 

12

 

TYPE OF REPORTING PERSON*

 

 
 

 

PN

    

 

 

 

 

  

CUSIP No. 53220K207

 

13G

 

Page 3 of 12 Pages

1

 

NAME OF REPORTING PERSON:
Biotechnology Value Fund II, L.P.

 

 
 

2

 

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

 (a)

 x

 

 

 

 (b)

o

 

 

 

 

 
 

3

 

SEC USE ONLY

 

 

 

 

 

 

 
 

4

 

CITIZENSHIP OR PLACE OF ORGANIZATION

 

 

Delaware

 

 

 

NUMBER OF

SHARES

BENEFICIALLY

OWNED

BY

EACH

REPORTING

PERSON

WITH:

          

 


5

 


SOLE VOTING POWER

 

 

 

0

 

  

 

6

 

SHARED VOTING POWER

 

 

  

1,611,000

 

  

 

7

 

SOLE DISPOSITIVE POWER

 

 

 

0

 

  

 

8

 

SHARED DISPOSITIVE POWER

 

 

 

1,611,000
 

9

 

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

 

 

 

 

1,611,000

 

 
 

10

 

CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*

 

o

 

 

 

 

 
 

11

 

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

 

 

 

 

1.70%

 

 
 

12

 

TYPE OF REPORTING PERSON*

 

 
 

 

PN

    

 

 

 

 

  

CUSIP No. 53220K207

 

13G

 

Page 4 of 12 Pages

1

 

NAME OF REPORTING PERSON:
BVF Investments, L.L.C.

 

 
 

2

 

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

 (a)

 x

 

 

 

 (b)

o

 

 

 

 

 
 

3

 

SEC USE ONLY

 

 

 

 

 

 

 
 

4

 

CITIZENSHIP OR PLACE OF ORGANIZATION

 

 

Delaware

 

 

 

NUMBER OF

SHARES

BENEFICIALLY

OWNED

BY

EACH

REPORTING

PERSON

WITH:

          

 


5

  


SOLE VOTING POWER

 

 

 

0

 

  

 

6

 

SHARED VOTING POWER

 

 

  

5,834,300

 

  

 

7

 

SOLE DISPOSITIVE POWER

 

 

 

0

 

  

 

8

 

SHARED DISPOSITIVE POWER

 

 

 

5,834,300
 

9

 

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

 

 

 

 

5,834,300

 

 
 

10

 

CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*

 

o

 

 

 

 

 
 

11

 

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

 

 

 

 

6.15%

 

 
 

12

 

TYPE OF REPORTING PERSON*

 

 
 

 

OO

    

 

 

 

 

  

CUSIP No. 53220K207

 

13G

 

Page 5 of 12 Pages

1

 

NAME OF REPORTING PERSON:
Investment 10, L.L.C.

 

 
 

2

 

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

 (a)

  x

 

 

 

 (b)

o

 

 

 

 

 
 

3

 

SEC USE ONLY

 

 

 

 

 

 

 
 

4

 

CITIZENSHIP OR PLACE OF ORGANIZATION

 

 

Illinois

 

 

 

NUMBER OF

SHARES

BENEFICIALLY

OWNED

BY

EACH

REPORTING

PERSON

WITH:

          

 


5

 


SOLE VOTING POWER

 

 

 

0

 

  

 

6

 

SHARED VOTING POWER

 

 

  

610,000

 

  

 

7

 

SOLE DISPOSITIVE POWER

 

 

 

0

 

  

 

8

 

SHARED DISPOSITIVE POWER

 

 

 

610,000
 

9

 

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

 

 

 

 

610,000

 

 
 

10

 

CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*

 

o

 

 

 

 

 
 

11

 

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

 

 

 

 

0.64%

 

 
 

12

 

TYPE OF REPORTING PERSON*

 

 
 

 

OO

    

 

 

 

 

  

CUSIP No. 53220K207

 

13G

 

Page 6 of 12 Pages

1

 

NAME OF REPORTING PERSON:
BVF Partners L.P.

 

 
 

2

 

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

 (a)

 x

 

 

 

 (b)

o

 

 

 

 

 
 

3

 

SEC USE ONLY

 

 

 

 

 

 

 
 

4

 

CITIZENSHIP OR PLACE OF ORGANIZATION

 

 

Delaware

 

 

 

NUMBER OF

SHARES

BENEFICIALLY

OWNED

BY

EACH

REPORTING

PERSON

WITH:

          

 


5

 


SOLE VOTING POWER

 

 

 

0

 

  

 

6

 

SHARED VOTING POWER

 

 

  

10,383,948

 

  

 

7

 

SOLE DISPOSITIVE POWER

 

 

 

0

 

  

 

8

 

SHARED DISPOSITIVE POWER

 

 

 

10,383,948
 

9

 

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

 

 

 

 

10,383,948

 

 
 

10

 

CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*

 

o

 

 

 

 

 
 

11

 

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

 

 

 

 

10.94%

 

 
 

12

 

TYPE OF REPORTING PERSON*

 

 
 

 

PN, HC

    

 

 

 

 

  

CUSIP No. 53220K207

 

13G

 

Page 7 of 12 Pages

1

 

NAME OF REPORTING PERSON:
BVF Inc.

 

 
 

2

 

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

 (a)

 x

 

 

 

 (b)

o

 

 

 

 

 
 

3

 

SEC USE ONLY

 

 

 

 

 

 

 
 

4

 

CITIZENSHIP OR PLACE OF ORGANIZATION

 

 

Delaware

 

 

 

NUMBER OF

SHARES

BENEFICIALLY

OWNED

BY

EACH

REPORTING

PERSON

WITH:

          

 


5

 


SOLE VOTING POWER

 

 

 

0

 

  

 

6

 

SHARED VOTING POWER

 

 

  

10,383,948

 

  

 

7

 

SOLE DISPOSITIVE POWER

 

 

 

0

 

  

 

8

 

SHARED DISPOSITIVE POWER

 

 

 

10,383,948
 

9

 

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

 

 

 

 

10,383,948

 

 
 

10

 

CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES*

 

o

 

 

 

 

 
 

11

 

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

 

 

 

 

10.94%

 

 
 

12

 

TYPE OF REPORTING PERSON*

 

 
 

 

CO, HC

    

 

 

 

 

  

CUSIP No. 53220K207

 

13G

 

Page 8 of 12 Pages

ITEM 1(a)

NAME OF ISSUER:    LIGAND PHARMACEUTICALS INCORPORATED (“LGND”)


 

ITEM 1(b)

ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES:

 

 

10275 Science Center Drive
 

San Diego, CA 92121-1117

 

ITEM 2(a).

NAME OF PERSON FILING:

 

  
 

This 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. ("BVLLC")

 

(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 Schedule 13G is located at 900 North Michigan Avenue, Suite 1100, Chicago, Illinois, 60611.
 

ITEM 2(c).

CITIZENSHIP:

 

 

 

BVF:

a Delaware limited partnership

 

 

BVF2:

a Delaware limited partnership

 

 

BVLLC:

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 Schedule 13G, is being filed with respect to the common stock, par value $0.001 per share ("Common Stock"), of LGND. The Reporting Persons' percentage ownership of Common Stock is based on 94,929,774 shares of Common Stock being outstanding.

 

As of November 6,  2008, BVF beneficially owned 2,328,648 shares of Common Stock, BVF2 beneficially owned 1,611,000 shares of Common Stock, BVLLC beneficially owned 5,834,300 shares of Common Stock, and ILL10 beneficially owned 610,000 shares of Common Stock. Partners and BVF Inc. may each be deemed to beneficially own 10,383,948 shares of Common Stock.

 

ITEM 2(e).

CUSIP Number:                 53220K207

 

 

 

 

 

  

CUSIP No. 53220K207

 

13G

 

Page 9 of 12 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 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) of this 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 owners of more than 5 percent of the class of securities, check the following [ ].
 

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

 Pursuant to the operating agreement of BVLLC, Partners is authorized, among other things, to invest the funds of Ziff Asset Management, L.P., the majority member of BVLLC, in the shares of Common Stock beneficially owned by BVLLC and to vote and exercise dispositive power over those shares of Common Stock. Partners and BVF Inc. share voting and dispositive power over shares of Common Stock beneficially owned by BVF, BVF2, BVLLC 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 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:
 

Mr. Lampert is the owner, sole director and an officer of BVF Inc. BVF Inc. is the general partner of Partners, which is the general partner of BVF and BVF 2. Partners is the manager of BVLLC and is investment adviser to ILL10.
 

ITEM 8.        IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF A GROUP:
 

The members of the group making this filing on Schedule 13G are: Biotechnology Value Fund, L.P., Biotechnology Value Fund II, L.P., BVF Investments, L.L.C., Investment 10, L.L.C., BVF Partners L.P. and BVF Inc.
 

ITEM 9.        NOTICE OF DISSOLUTION OF GROUP:
 

Not applicable.
 

 

 

 

 

  

CUSIP No. 53220K207

 

13G

 

Page 10 of 12 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: November 7, 2008

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 investment manager

 

  
 

By:

BVF Inc., its general partner

 

    
 

By:

/s/ Mark N. Lampert
   

Mark N. Lampert, President

 

BVF PARTNERS L.P.*
 

By:

BVF Inc., its general partner

 

  
 

By:

/s/ Mark N. Lampert
   

Mark N. Lampert, President
   

 

BVF INC.*

 

  
 

By:

/s/ Mark N. Lampert
   

Mark N. Lampert, President
   

 


 
 

*The Reporting Person disclaims beneficial ownership except to the extent of its pecuniary interest therein.

Exhibit A
JOINT FILING AGREEMENT

The undersigned agree that Schedule 13G, dated November 7, 2008, relating to the Common Stock of LGND shall be filed on behalf of the undersigned.

Dated: November 7, 2008

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 investment manager

 

  
 

By:

BVF Inc., its general partner

 

    
 

By:

/s/ Mark N. Lampert
   

Mark N. Lampert, President


BVF PARTNERS L.P.
 

By:

BVF Inc., its general partner

 

  
 

By:

/s/ Mark N. Lampert
   

Mark N. Lampert, President


BVF INC.
 

 

By:

/s/ Mark N. Lampert
   

Mark N. Lampert, President