8-K

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d) of The

Securities Exchange Act of 1934

Date of Report (Date of earliest event reported): March 29, 2012

LIGAND PHARMACEUTICALS INCORPORATED

(Exact name of registrant as specified in its charter)

Delaware	001-33093	77-0160744
(State or other jurisdiction of Incorporation)	(Commission File Number)	(I.R.S. Employer Identification No.)

11085 North Torrey Pines Road, Suite 100, La Jolla, California 92037

(Address of principal executive offices) (Zip Code)

(858) 550-7500

(Registrant’s telephone number, including area code)

N/A

(Former Name or Former Address, if Changed Since Last Report)

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:

¨ Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)

¨ Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)

¨ Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))

¨ Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))

Item 1.01 Entry into a Material Definitive Agreement.

As previously announced, on March 31, 2011, Ligand Pharmaceuticals Incorporated (“Ligand”) entered into a Loan and Security Agreement (the “Square 1 Loan and Security Agreement”) with Square 1 Bank (“Square 1”). The Square 1 Loan and Security Agreement established a cash-collateralized revolving line of credit facility under which Square 1 shall loan up to $5,000,000 to Ligand; Ligand immediately borrowed the full $5,000,000. All outstanding amounts under the Square 1 Loan and Security Agreement bear interest at a floating rate equal to 200 basis points above the prime rate. Interest is payable on a monthly basis. The maturity date of the revolving line of credit facility is March 29, 2012.

In addition, as previously announced, on April 29, 2011, Ligand and Square 1 entered into a First Amendment to Loan and Security Agreement (the “Square 1 First Amendment to Loan and Security Agreement”). The Square 1 First Amendment to Loan and Security Agreement increased the Loan and Security Agreement’s cash-collateralized revolving line of credit facility from $5,000,000 to $10,000,000; Ligand immediately borrowed the full additionally-authorized $5,000,000. The Square 1 First Amendment to Loan and Security Agreement did not change the interest rate, interest payment schedule and maturity date established in the Square 1 Loan and Security Agreement.

In addition, as previously announced, on January 20, 2012 Ligand prepaid $4,500,000 of principal pursuant to the Square 1 Loan and Security Agreement, as amended. In addition, on March 7, 2012 Ligand prepaid an additional $4,000,000 of principal pursuant to the Square 1 Loan and Security Agreement, as amended.

On March 29, 2012, Ligand and Square 1 entered into a Second Amendment to Loan and Security Agreement (the “Square 1 Second Amendment to Loan and Security Agreement”). The Square 1 Second Amendment to Loan and Security Agreement changed the maturity date of the revolving line of credit facility to March 28, 2013. The Square 1 Second Amendment to Loan and Security Agreement did not change the interest rate and interest payment schedule established in the Loan and Security Agreement.

The foregoing summary of the material terms of the Square 1 Second Amendment to Loan and Security Agreement does not purport to be complete and is qualified in its entirety by reference to the Square 1 Second Amendment to Loan and Security Agreement, a copy of which is filed as Exhibit 10.1 hereto and incorporated herein by reference.

Item 9.01 Financial Statements and Exhibits.

(d) Exhibits.

The following exhibit is attached to this Current Report on Form 8-K:

Exhibit No.	Description
10.1	Second Amendment to Loan and Security Agreement, by and between Ligand Pharmaceuticals Incorporated and Square 1 Bank, dated March 29, 2012

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 hereunto duly authorized.

	LIGAND PHARMACEUTICALS INCORPORATED
Date: April 4, 2012
	By:	/s/ Charles S. Berkman
	Name:	Charles S. Berkman
	Title:	Vice President, General Counsel and Secretary

EXHIBIT INDEX

Exhibit No.	Description
10.1	Second Amendment to Loan and Security Agreement, by and between Ligand Pharmaceuticals Incorporated and Square 1 Bank, dated March 29, 2012

EX-10.1

Exhibit 10.1

SECOND AMENDMENT

TO

LOAN AND SECURITY AGREEMENT

This Second Amendment to Loan and Security Agreement (the “Amendment”), is entered into as of March 29, 2012, by and between SQUARE 1 BANK (the “Bank”) and LIGAND PHARMACEUTICALS INCORPORATED (the “Borrower”).

RECITALS

Borrower and Bank are parties to that certain Loan and Security Agreement dated as of March 31, 2011 (as amended from time to time, the “Agreement”). The parties desire to amend the Agreement in accordance with the terms of this Amendment.

NOW, THEREFORE, the parties agree as follows:

1) Section 6.3 of the Agreement is hereby amended and restated, in its entirety, as follows:

6.3 Cash Security Account. Borrower shall at all times maintain the Cash Security Account, with a balance of Cash in such Cash Security Account at all times of not less than the total amount outstanding under the Revolving Line.

2) The following definitions in Exhibit A to the Agreement are hereby amended and restated, in their entirety, as follows:

“Cash Security Account” means segregated money market account no. 7002291, held at Bank as collateral for Borrower’s Obligations, in an amount equal to or greater than the total amount outstanding under the Revolving Line.

“Collateral” means Cash held in the Cash Security Account and pledged to Bank as security for the Obligations, which shall at all times be in an amount equal to or greater than the total amount outstanding under the Revolving Line.

“Revolving Maturity Date” means March 28, 2013.

3) Unless otherwise defined, all initially capitalized terms in this Amendment shall be as defined in the Agreement. The Agreement, as amended hereby, shall be and remain in full force and effect in accordance with its respective terms and hereby is ratified and confirmed in all respects. Except as expressly set forth herein, the execution, delivery, and performance of this Amendment shall not operate as a waiver of, or as an amendment of, any right, power, or remedy of Bank under the Agreement, as in effect prior to the date hereof. Borrower ratifies and reaffirms the continuing effectiveness of all agreements entered into in connection with the Agreement.

4) Borrower represents and warrants that the representations and warranties contained in the Agreement are true and correct as of the date of this Amendment.

Ligand Pharmaceuticals Incorporated – 2^nd Amendment to LSA

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5) This Amendment may be executed in two or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one instrument.

6) As a condition to the effectiveness of this Amendment, Bank shall have received, in form and substance satisfactory to Bank, the following:

a) this Amendment, duly executed by Borrower;

b) an officer’s certificate of Borrower with respect to incumbency and resolutions authorizing the execution of this Amendment;

c) payment of all Bank Expenses, including Bank’s expenses for the documentation of this Amendment and any related documents, and any UCC, good standing and intellectual property search or filing fees, which may be debited from any of Borrower’s accounts; and

d) such other documents and completion of such other matters, as Bank may reasonably deem necessary or appropriate.

[Signature Page Follows]

Ligand Pharmaceuticals Incorporated – 2^nd Amendment to LSA

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IN WITNESS WHEREOF, the undersigned have executed this Amendment as of the first date above written.

LIGAND PHARMACEUTICALS INCORPORATED		SQUARE 1 BANK
By:	/s/ John Sharp	By:	/s/ Patrick Cahill
Name:	John Sharp	Name:	Patrick Cahill
Title:	CFO	Title:	AVP

[Signature Page to Second Amendment to Loan and Security Agreement]

Ligand Pharmaceuticals Incorporated – 2^nd Amendment to LSA

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