X0303 4 2009-02-17 0 0000886163 LIGAND PHARMACEUTICALS INC LGND 0000808722 KNOTT DAVID M 485 UNDERHILL BLVD STE 205 SYOSSET NY 11791-3419 1 0 0 0 Common Stock 2009-02-17 4 P 0 511800 2.6 A 3369983 I By Knott Partners, L.P. Common Stock 2009-02-17 4 S 0 235500 4.6 D 1521941 I By Shoshone Partners, L.P. Common Stock 2009-02-17 4 P 0 240000 2.6 A 267600 I By Mulsanne Partners, L.P. Common Stock 2009-02-17 4 S 0 591100 4.6 D 2704228 I By Knott Partners Offshore Master Fund, L.P. Common Stock 259184 I By Ostra Capital Partners, L.P. Common Stock 2009-02-17 4 P 0 59400 2.6 A 185290 I By Managed Accounts A Common Stock 2009-02-17 4 P 0 15400 2.6 A 118931 I By Managed Accounts B Common Stock 4000 I By Managed Accounts C Common Stock 69500 I By Managed Accounts D Common Stock 10000 D Common Stock 82400 I By Ostra Capital Partners VII, L.P. The Reporting Person is the managing member of Knott Partners Management, LLC, which is (i) the sole general partner of Shoshone Partners, L.P., Knott Partners Offshore Master Fund, 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 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 securities identified in this row are held by a managed account for which Dorset Management Corporation provides portfolio management services. The Reporting Person is the President and sole director of Dorset Management Corporation. The securities reported in Column 4 of Table I represent restricted shares of Common Stock of Ligand Pharmaceuticals, granted to all directors at the annual meeting of the shareholders on May 29, 2008. The restricted stock vests on the first anniversary of the date of grant. 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., Knott Partners Offshore Master Fund, 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 Knott Partners, L.P., Shoshone Partners, L.P., Mulsanne Partners, L.P., Knott Partners Offshore Master Fund, L.P., Ostra Capital Partners, L.P., Ostra Capital Partners VII, L.P. and each of the Managed Accounts disclaims beneficial ownership of securities reported as owned by any other party. Each entry reports a component of a cross transaction in the common stock described in footnote 1 among the accounts identified in Column 7 of Table I that are coded P or S in Column 3. The cross transactions reported reflect a reallocation of common stock among those accounts, and the accounts that disposed of common stock in the cross transaction did not acquire any common stock in the cross transaction. /s/ David M. Knott 2009-02-19