Document:

First Amendment to Lease, dated May 10, 2005

 EXHIBIT 10.54 
  
 FIRST AMENDMENT TO LEASE 
  
 THIS FIRST AMENDMENT TO LEASE (this “Amendment”), dated as of May 10, 2005 (the “Amendment Date”), is entered into by
and between BMR-201 Industrial Road LLC, a Delaware limited liability company (“Landlord”), and Nuvelo, Inc., a Delaware corporation (“Tenant”). Landlord and Tenant shall each be referred to herein as a
“Party” and collectively as the “Parties.” Capitalized terms not otherwise defined herein shall have the meanings assigned to them in the Original Lease (as defined below). 
  
 RECITALS 
  
 WHEREAS, Landlord and Tenant are parties to that certain Lease dated as of January 11, 2005 (the “Original
Lease”), pursuant to which Tenant leases from Landlord certain space (the “Original Premises”) located in the Project; and 
  
 WHEREAS, the Parties desire to amend the Original Lease, among other matters, and to increase and confirm the square footage of the Premises. 

 
 NOW, THEREFORE, for good and valuable consideration, the receipt and
sufficiency of which are hereby acknowledged, the Parties hereby agree as follows: 
  
 AMENDMENT 
  
 1.
Additional Premises. Tenant hereby leases from Landlord, and Landlord hereby leases to Tenant, additional space in the Project (the “Additional Premises”). From and after the Amendment Date, (a) the term “Premises,”
when used in the Lease (as defined below), shall include the Original Premises and the Additional Premises, as shown on Exhibit B-1 hereto, and (b) Exhibit B-1 to this Amendment shall replace Exhibit B-1 to the Original Lease in
its entirety. From and after the Amendment Date, the total “Rentable Area” under Section 2 of the Original Lease shall equal sixty-one thousand eight hundred twenty-six (61,826) rentable square feet. 
  
 2. Rent on Additional Premises. Commencing on the Rent Commencement
Date, Tenant shall pay Rent on the Additional Premises at the rate set forth in the Original Lease for the Premises. The Rent Commencement Date for the Additional Premises shall be deemed to be the same as the Rent Commencement Date for the Original
Premises, and the initial Lease Term for the Additional Premises shall expire on the same date as the initial Lease Term for the Original Premises. “Tenant’s Pro Rata Share of Operating Expenses,” as set forth in Section 2 of
the Original Lease, shall equal seventy and one hundredth percent (70.01%) with respect to Operating Expenses for the Building, and thirty-seven and seventy-three hundredths percent (37.73%) with respect to Operating Expenses for the Project.

  
 3. Delivery of Additional Premises. Upon execution of
this Amendment, Landlord shall deliver the Additional Premises to Tenant for construction of Tenant Improvements. 
  
 4. Increase in Security Deposit. Tenant shall increase the amount of the Security Deposit to Four Hundred Thirty-Five Thousand Eight Hundred
Seventy-Four Dollars ($435,874) (the “Increased Security Deposit”). Upon execution of this Amendment, Tenant shall deposit with Landlord the difference between the Increased Security Deposit and the Security Deposit required under
the Original Lease. The provisions in the Original Lease applicable to the Security Deposit shall apply to the increase in the Security Deposit required by this Section 4. 

 5. Increase in Tenant Improvement Allowance. Tenant shall be entitled to an increase in the Tenant
Improvement Allowance of One Hundred Forty Dollars ($140) per rentable square foot for the Additional Premises, increasing the total Tenant Improvement Allowance under the Lease to Eight Million Six Hundred Fifty-Five Thousand Six Hundred Forty
Dollars ($8,655,640), the use and terms of which shall be governed by the Original Lease. If not used by Tenant prior to the date that is twelve (12) months after the Rent Commencement Date, Tenant shall forfeit the right to such increase in the
Tenant Improvement Allowance. 
  
 6. Expansion Option.
Section 29.1 of the Original Lease is amended by replacing “[10,000]” with “seven thousand six hundred twenty-four (7,624)”. Exhibit G to the Original Lease is hereby replaced in its entirety with Exhibit G attached
hereto. Tenant’s Pro Rata Share of Operating Expenses for the Expansion Space, if Tenant exercises the Expansion Option, would be eight and sixty-three hundredths percent (8.63%) with respect to Operating Expenses for the Building, and four and
sixty-five hundredths percent (4.65%) with respect to Operating Expenses for the Project. 
  
 7. Confirmation of Exhibits. The Parties agree that (a) Exhibit A attached hereto constitutes Exhibit A to the Original Lease, (b) Exhibit B attached hereto constitutes Exhibit B to
the Original Lease, (c) Exhibit B-2 attached hereto constitutes Exhibit B-2 to the Original Lease, (d) Exhibit E attached hereto constitutes Exhibit E to the Original Lease and (e) Exhibit F attached hereto
constitutes Exhibit F to the Original Lease. 
  
 8.
Lease Defined. Except as expressly amended by this Amendment, the Lease shall remain unmodified and in full force and effect, enforceable in accordance with its terms. From and after the Amendment Date, the term “Lease,” when used
in the Lease, shall mean the Lease as amended by this Amendment. 
  
 9. Counterparts. This Amendment may be executed in one or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument executed on the date first set forth.

  
 10. Authorization. Each individual executing this
Amendment on behalf of its respective party represents and warrants that the execution and delivery of this Amendment on behalf of such party is duly authorized, and that he or she is authorized to execute and deliver this Amendment on behalf of
such party. 
  
 [REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK]

  
  

 IN WITNESS WHEREOF the parties hereto have signed this Amendment as of the date first above written.

  
 LANDLORD: 
  
 BMR-201 INDUSTRIAL ROAD LLC, 
 a Delaware
limited liability company 

			
		
	By:	 	 /s/ Gary A. Kreitzer

	Name:	 	 Gary A. Kreitzer

	Its:	 	 Executive V.P.

  
 TENANT: 
 NUVELO, INC., 
 a Delaware corporation 

			
		
	By:	 	 /s/ Lee Bendekgey

	Name:	 	 Lee Bendekgey

	Title:	 	 Senior Vice President, Chief Financial

	 	 	 Officer, and General Counsel2005 Executive Bonus Structure

 Exhibit 10.30 
  
 2005 Executive Bonus Structure 
  
 Criteria (100% of eligible bonus as follows) 
  

	 	•	 	65% tied to targeted pre-tax profit levels set by the Compensation Committee based on the Company’s prior year results and Plan for the current year, with payment amounts of
zero, 50%, 75% or 100% based on performance levels against that Plan. 

  

	 	•	 	35% tied to performance against individual MBOs with certain minimum pretax target requirements set by the Compensation Committee. 

  
 Opportunity 
  

	 	•	 	25-35% of annual base salary (depending upon executive) 

  
 Other 
  

	 	•	 	Additional upside opportunity of 2% to 5% of annual base salary if pre-tax profits reach levels established by the Compensation Committee in excess of the Company’s Plan.Employment Letter Agreement

 Exhibit 10.19 
  
 Threshold 
 Pharmaceuticals

  
 October 25, 2004 
  
 Alan Colowick, M.D. 
 10 Bellerivehohe 
 6006 Luzern, Switzerland 
  

	Re:	Employment Terms 

  
 Dear Alan, 
  
 This letter confirms that Threshold
Pharmaceuticals, Inc. (the “Company”) has offered you the position of Chief Medical Officer (CMO) beginning on January 15, 2005 on the following terms: 
  
 You will report to Barry Selick, Chief Executive Officer (CEO) and work at our facility located at 1300 Seaport Blvd, Redwood City, CA
94063. Of course, the Company may change your position, duties and work location from time to time as it deems necessary. 
  
 Your compensation will be $25,000 per month, less payroll deductions and all required withholdings. You will be paid semi-monthly and will be eligible for standard
Company benefits as outlined on the attached Employee Benefits Program summary. The Company may modify compensation and benefits from time to time as it deems necessary. In addition, the Company will provide you with a two part sign-on bonus
totaling $300,000, less all required withholdings. This first installment of your sign-on bonus, in the amount of $200,000 less all required withholding, will be paid to you on your start date and is subject to repayment in full if you voluntarily
leave the Company before your one year anniversary date. The second and final installment of your sign-on bonus, in the amount of $100,000 less all required withholdings will be paid to you on your one year anniversary date and is subject to
repayment in full if you voluntarily leave the Company before your two year anniversary date. To assist you in your relocation transition, the Company will provide you with two (2) weekend house hunting trips for you and your spouse, corporate
housing for up to three (3) months and will pay for the relocation of your bulk goods. Additionally, the Company will provide you with $7,000 less all required withholdings, to assist you in fulfilling your vehicle lease terms. This $7,000 is
subject to repayment in full if you leave the Company voluntarily before your one year anniversary date. 
  
 Subject to the approval of the Company’s Board of Directors, you will be awarded a stock option grant to purchase 250,000 shares of the Company’s Common Stock subject to a four year vesting schedule as
follows: (a) the first 25% of this grant shall vest at the one year anniversary of your starting date with the Company and (b) thereafter an additional 1/48th of the grant shall vest on each subsequent monthly anniversary of your starting date. The
exercise price of your stock option will be equal to the fair market value of the Company’s Common Stock on the date your option is approved by the Board of Directors. 
  
 As a Company employee, you will be expected to abide by Company rules and regulations, sign and comply with the attached Proprietary
Information and Inventions Agreement which prohibits unauthorized use or disclosure of Company proprietary information and, once it is available, acknowledge in writing that you have read the Company’s Employee Handbook. 
  

 Alan Colowick, M.D. 
 Page 2 of 2 
  
 In your work for the Company, you will be expected not to use or disclose any confidential information, including trade secrets, of any former employer or other person to whom you have an obligation of confidentiality. Rather, you will be
expected to use only that information which is generally known and used by persons with training and experience comparable to your own, which is common knowledge in the industry or otherwise legally in the public domain, or which is otherwise
provided or developed by the Company. During our discussions about your proposed job duties, you assured us that you would be able to perform those duties within the guidelines just described. 
  
 You agree that you will not bring onto Company premises any unpublished documents or property
belonging to any former employer or other person to whom you have an obligation of confidentiality. 
  
 You may terminate your employment with the Company at any time and for any reason whatsoever simply by notifying the Company. Likewise, the Company may terminate your employment at any time and for any reason
whatsoever, with or without cause or advance notice. As required by law, this offer is subject to satisfactory proof of your right to work in the United States. A “List of Acceptable Documents” for employment eligibility verification is
attached for your information. 
  
 This letter, together with your Proprietary
Information and Inventions Agreement, forms the complete and exclusive statement of your employment agreement with the Company. The employment terms in this letter supersede any other agreements or promises made to you by anyone, whether oral or
written. This letter agreement cannot be changed except in writing signed by you and a duly authorized officer of the Company. 
  
 Please indicate your acceptance of our offer by signing below and returning the original copy of this letter of employment from Threshold Pharmaceuticals under the terms
described above. Should you have any questions, please contact me at 650-553-8911. 
  
 We look forward to your favorable reply and to a productive and enjoyable work relationship. 
  

	
	 Sincerely,

	
	 /s/ Harold E. Selick, Ph.D.

	 Harold E. Selick, Ph.D.

	 CEO

  

					
	 Accepted:
	 	 	 	 
			
	 /s/ Alan Colowick, M.D.
	 	 	 	 Dec-22-04

	 Alan Colowick, M.D.
	 	 	 	 Date

  

			
	Enclosures:	  	Proprietary Information and Inventions Agreement
	 	  	Employee Benefits Summary
	 	  	I-9 List of Acceptable Documents

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