ANACOR PHARMACEUTICALS, INC. CONSULTING AGREEMENT

Exhibit 10.10

ANACOR PHARMACEUTICALS, INC.

CONSULTING AGREEMENT

        This Consulting Agreement (the " Agreement ") is entered into by and between Anacor Pharmaceuticals, Inc., a Delaware corporation (the " Company "), and Stephen J. Benkovic, Ph.D. (" Consultant ").

        1.     Consulting Relationship.     During the term of this Agreement, Consultant will provide consulting services (the " Services ") to the Company as described on Exhibit A attached to this Agreement. Consultant represents that Consultant is duly licensed (as applicable) and has the qualifications, the experience and the ability to properly perform the Services. Consultant shall use Consultant's best efforts to perform the Services such that the results are satisfactory to the Company. Consultant shall devote at least 20% of Consultant's time to performance of the Services.

        2.     Fees.     As consideration for the Services to be provided by Consultant and other obligations, the Company shall pay to Consultant the amounts specified in Exhibit B attached to this Agreement at the times specified therein.

        3.     Expenses.     Consultant shall not be authorized to incur on behalf of the Company any expenses , except as expressly specified in Exhibit B, without the prior consent of the Company's Chief Executive Officer, which consent shall be evidenced in writing for any expenses in excess of $1,000.00. As a condition to receipt of reimbursement, Consultant shall be required to submit to the Company reasonable evidence that the amount involved was expended and related to Services provided under this Agreement.

        4.     Term and Termination.     Consultant shall serve as a consultant to the Company for a period commencing on April 1, 2007 and terminating on March 31, 2008; provided , however , that the Consulting Relationship shall terminate prior to such date if (a) Consultant completes the provision of the Services to the Company under this Agreement, or (b) Consultant shall have been paid the maximum amount of consulting fees as provided in Exhibit B . Notwithstanding the foregoing, either party may terminate this Agreement at any time upon ten (10) days' written notice. In the event of such early termination, Consultant shall be paid for any portion of the Services that have been performed prior to the termination.

        5.     Independent Contractor.     Consultant's relationship with the Company will be that of an independent contractor and not that of an employee.

•         (a)     Method of Provision of Services.     Consultant shall be solely responsible for determining the method, details and means of performing the Services. Consultant may, at Consultant's own expense, employ or engage the service of such employees or subcontractors as Consultant deems necessary to perform the Services required by this Agreement (the " Assistants "). Such Assistants are not the employees of the Company and Consultant shall be wholly responsible for the professional performance of the Services by his Assistants such that the results are satisfactory to the Company. Consultant shall expressly advise the Assistants of the terms of this Agreement, and shall require each Assistant to execute a Confidential Information and Invention Assignment Agreement substantially in the form attached to this Agreement as Exhibit C (the " Confidentiality Agreement ").

          (b)     No Authority to Bind Company.     Neither Consultant, nor any partner, agent or employee of Consultant, has authority to enter into contracts that bind the Company or create obligations on the part of the Company without the prior written authorization of the Company.

          (c)     No Benefits.     Consultant acknowledges and agrees that Consultant (or Consultant's employees, if Consultant is an entity) will not be eligible for any Company employee benefits and, to the extent Consultant (or Consultant's employees, if Consultant is an entity) otherwise would be eligible for any Company employee benefits but for the express terms of this Agreement,

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  Consultant (on behalf of itself and its employees) hereby expressly declines to participate in such Company employee benefits.

          (d)     Withholding; Indemnification.     Consultant shall have full responsibility for applicable withholding taxes for all compensation paid to Consultant, its partners, agents or its employees under this Agreement, and for compliance with all applicable labor and employment requirements with respect to Consultant's self-employment, sole proprietorship or other form of business organization, and Consultant's partners, agents and employees, including state worker's compensation insurance coverage requirements and any US immigration visa requirements. Consultant agrees to indemnify, defend and hold the Company harmless from any liability for, or assessment of, any claims or penalties with respect to such withholding taxes, labor or employment requirements, including any l