X0306 4 2013-06-11 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 972100 I By Knott Partners, L.P. Common Stock 264661 I By Shoshone Partners, L.P. Common Stock 211396 I By Knott Partners Offshore Master Fund, L.P. Common Stock 1666 I By Managed Account C Common Stock 2013-06-11 4 A 0 4318 0.00 A 63743 D Common Stock 2743 I By immediate family member Non-Qualified Stock Option (right to buy) 32.30 2013-06-11 4 A 0 7335 0.00 A 2023-06-11 Common Stock 7335 7335 D Non-Qualified Stock Option (right to buy) 12.53 2022-05-31 Common Stock 7335 7335 D The Reporting Person is the managing member of Knott Partners Management, LLC, which is (a) the sole general partner of Shoshone Partners, L.P., and Knott Partners Offshore Master Fund, L.P. and (b) 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 director and the president of Dorset Management Corporation, which provides investment management services to separate institutional managed accounts (each, a "Managed Account"), and (b) the spouse of the immediate family member (the "Spouse"). 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 over the securities in this entry. Except with respect to those securities held by the Spouse, the Reporting Person may be deemed indirectly to beneficially own the securities in this entry as a result of a performance related fee. Except with respect to the Reporting Person's beneficial interest in Knott Partners, L.P., Knott Partners Offshore Master Fund, L.P., and Shoshone Partners, L.P., the Reporting Person disclaims beneficial ownership of the securities beneficially owned by the Managed Account, except to the extent ultimately realized. Each of Knott Partners, L.P., Knott Partners Offshore Master Fund, L.P., Shoshone Partners, L.P., the Managed Account and the Spouse disclaims beneficial ownership of securities reported as owned by any other party. These securities, as represented in Columns 4 and 5, represent (a) 1393 restricted shares issued in lieu of annual cash retainer at the Company's annual meeting of its shareholders on June 11, 2013 (the "2013 Meeting"), which shares are immediately vested, and (b) 2,925 restricted shares acquired by a grant of the Board of Directors of the Company at the 2013 Meeting, which shares will vest in full on the first anniversary of the grant date. These securities, as represented in Column 5, were acquired by a grant of 7,335 shares by the Board of Directors of the Company at the 2013 Meeting. That grant vests in full on the first anniversary of the grant date or immediately (x) upon a change in control or a hostile takeover of the Company or (y) the death or permanent disability of the grantee if still serving at that time. These securities were previously reported on a Form 4 for this Reporting Person filed on June 4, 2012, and are included on this Form 4 only to report that they are now fully vested and exercisable. /s/David M. Knott 2013-06-13