X0202 4/A 2006-11-29 2006-12-01 1 0000886163 LIGAND PHARMACEUTICALS INC LGND 0000808722 KNOTT DAVID M 485 UNDERHILL BLVD STE 205 SYOSSET NY 11791-3419 0 0 1 0 Common Stock 2006-11-29 4 C 0 148383 6.1732 A 2419383 I By Knott Partners, L.P. Common Stock 2006-11-29 4 C 0 70141 6.1732 A 1326841 I By Shoshone Partners, L.P. Common Stock 18400 I By Mulsanne Partners, L.P. Common Stock 2006-11-29 4 C 0 140931 6.1732 A 3929331 I By Matterhorn Offshore Fund Limited Common Stock 2006-11-29 4 C 0 259184 6.1732 A 291584 I By Ostra Capital Partners, L.P. Common Stock 153830 I By Richard Murawczyk Common Stock 2006-11-29 4 C 0 29318 6.1732 A 478018 I By Managed Accounts 6% Convertible Subordinated Notes due 2007 6.1732 2006-11-29 4 C 0 916000 0 D 2002-11-26 2007-11-16 Common Stock 148383 0 I By Knott Partners, L.P. 6% Convertible Subordinated Notes due 2007 6.1732 2006-11-29 4 C 0 433000 0 D 2002-11-26 2007-11-16 Common Stock 70141 0 I By Shoshone Partners, L.P. 6% Convertible Subordinated Notes due 2007 6.1732 2006-11-29 4 C 0 870000 0 D 2002-11-26 2007-11-16 Common Stock 140931 0 I By Matterhorn Offshore Fund Limited 6% Convertible Subordinated Notes due 2007 6.1732 2006-11-29 4 C 0 1600000 0 D 2002-11-26 2007-11-16 Common Stock 259184 0 I By Ostra Capital Partners, L.P. 6% Convertible Subordinated Notes due 2007 6.1732 2006-11-29 4 C 0 181000 0 D 2002-11-26 2007-11-16 Common Stock 29318 0 I By Managed Accounts The Reporting Person is the managing member of Knott Partners, Management, LLC, which is (i) the sole general partner of Shoshone Partners, L.P. and Mulsanne Partners, L.P. and (ii) the managing general partner of Knott Partners, L.P. The Reporting Person is also a general partner of Knott Partners, L.P. The Reporting Person is the sole shareholder, director and president of Dorset Management Corporation, which (i) provides investment management services to Matterhorn Offshore Fund Limited and (ii) is the employer of Richard Murawczyk, the managing member of the general partner of Ostra Capital partners, L.P. and Ostra Capital Partners VII, L.P., with which Dorset Management Corporation has a trading relationship. The entry represents securities of the issuer held by managed accounts for which Dorset Management Corporation provides investment management services (the "Managed Accounts"). As a result of the Reporting Person's interests in Knott Partners Management, LLC and in Dorset Management Corporation, the Reporting Person has investment discretion and control of the securities represented in this entry. The Reporting Person may be deemed to beneficially own an indirect pecuniary interest in the securities represented in this entry as a result of its performance-related fee. Except with respect to Knott Partners, L.P. and Shoshone Partners, L.P., in which the Reporting Person owns a beneficial interest, the Reporting Person disclaims beneficial ownership therein except to the extent ultimately realized. Each of the Knott Partners, L.P., Shoshone Partners, L.P., Mulsanne Partners, L.P., Matterhorn Offshore Fund limited, Ostra Capital Partners, L.P., Ostra Capital Partners VII, L.P. and the Managed Accounts disclaims beneficial ownership of securities reported as owned by any other party. The Reporting Person ceased to be a 10% owner of the issuer on November 29, 2006 upon the public announcement by the issuer that the total number of issued and outstanding shares of common stock of the issuer had increased by 20,759,071 shares. /s/ David M. Knott 2006-12-05