UNITED STATES


SECURITIES AND EXCHANGE COMMISSION


Washington, D.C.  20549


________________________________________________________________________________________


FORM 10-Q/A


Amendment No. 1


________________________________________________________________________________________ xQuarterly Report Pursuant to Section 13 or 15 (d) of the Securities Exchange Act of 1934


For the quarterly period ended June 30, 2011


or oTransition Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934


For the Transition Period From ______ to ______ .


Commission File Number: 001-33093


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LIGAND PHARMACEUTICALS INCORPORATED


(Exact name of registrant as specified in its charter)


________________________________________________________________________________________


Delaware77-0160744(State or other jurisdiction ofincorporation or organization)(I.R.S. EmployerIdentification No.)3911 Sorrento Valley Boulevard,  Suite 110 San Diego, CA92121(Zip Code)(Address of principal executive offices)


(858) 550-7500


(Registrant's Telephone Number, Including Area Code)


________________________________________________________________________________________


Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes x No o


Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes x No o


Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company.  See definitions of  “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.  (Check one) Large Accelerated FilerxAccelerated FileroNon-Accelerated Filero(Do not check if a smaller reporting company)Smaller Reporting CompanyoEmerging Growth Companyo


Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes o No x


As of August 1, 2011, the registrant had 19,673,100 shares of common stock outstanding.





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EXPLANATORY NOTE





Ligand Pharmaceuticals Inc. (“Ligand” or the “Company”) is filing this Amendment No. 1 on Form 10-Q/A (the “Amendment”) to its Quarterly Report on Form 10-Q for the fiscal quarter ended June 30, 2011 (the “Original Form 10-Q”), originally filed with the Securities and Exchange Commission (the “Commission”) on August 8, 2011, in response to comments received from the Commission in connection with a request for confidential treatment of certain portions of Exhibit 10.27 to the Original Form 10-Q. Item 6 of Part II of the Original Form 10-Q is hereby amended to include an Exhibit Index and a revised redacted version of Exhibit 10.27, which is being filed herewith. In addition, as required by Rule 12b-15 under the Securities Exchange Act of 1934, as amended, new certifications by our principal executive officer and principal financial officer are filed as exhibits to this Amendment.





Except as described above, no other changes have been made to the Original Form 10-Q. This Amendment speaks as of the original filing date of the Original Form 10-Q and does not reflect any events that occurred at a date subsequent to the filing of the Original Form 10-Q or modify or update those disclosures therein in any way.








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|PART II. | OTHER INFORMATION




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|ITEM 6. | EXHIBITS




EXHIBIT INDEX





Exhibit NumberDescription10.27†Supply Agreement dated June 13, 2011 by and between CyDex and Merck31.3Certification by Principal Executive Officer, Pursuant to Rules 13a-14(a) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.31.4Certification by Principal Financial Officer, Pursuant to Rules 13a-14(a) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.


†  Confidential treatment has been requested for portions of this exhibit. These portions have been omitted and submitted separately to the Securities and Exchange Commission.





SIGNATURES


Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.





Date: November 1, 2017By:/s/ Matthew KorenbergMatthew KorenbergVice President, Finance and Chief Financial OfficerDuly Authorized Officer and Principal Financial Officer








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