Document:

Third Amendment to Lease

 Exhibit 10.9 
 THIRD AMENDMENT TO LEASE 
 THIS THIRD AMENDMENT TO LEASE (this
“Third Amendment”) is made as of October 3, 2012 (the “Effective Date”), by and between ARE-SAN FRANCISCO NO. 33, LLC, a Delaware limited liability company (“Landlord”), and ELAN
PHARMACEUTICALS, INC., a Delaware corporation (“Tenant”). 
 RECITALS 

A. Landlord and Tenant are parties to that certain Lease Agreement dated as of March 18, 2010, as amended by that certain
Letter Agreement dated as of March 18, 2010, as further amended by that certain First Amendment to Lease dated as of November 18, 2011, and as further amended by that certain Second Amendment to Lease dated June 1, 2012 (as amended,
the “Lease”). Pursuant to the Lease, Tenant leases certain premises consisting of approximately 27,550 rentable square feet (the “Existing Premises”) in a building located at 650 Gateway Boulevard, South San
Francisco, California (“Building”). The Existing Premises are comprised of (i) that certain portion of the Building containing approximately 26,299 rentable square feet (the “Original Premises,” as shown on
Exhibit A to the Lease), and (ii) that certain portion of the Building containing approximately 1,251 rentable square feet (the “Additional Premises,” as shown on Exhibit A to the Lease). Capitalized terms used
herein without definition shall have the meanings defined for such terms in the Lease. 
 B. Tenant desires to expand the
Existing Premises to include that certain portion of the Building consisting of approximately 8,891 rentable square feet, as shown on Exhibit A attached hereto (‘Second Expansion Premises”). 

C. Landlord and Tenant desire to and hereby amend Section 39(a) of the Lease in connection with Tenant’s
Expansion Right with respect to the Second Expansion Premises to delete the requirement for the existence of a Pending Deal or the delivery to Tenant of a Pending Deal Notice so that Tenant may exercise its Expansion Right with respect to the Second
Expansion Premises without the existence of a Pending Deal or the delivery to Tenant of a Pending Deal Notice. 
 D.
Landlord and Tenant desire, subject to the terms and conditions set forth below, to amend the Lease to, among other things, expand the Existing Premises by adding the Second Expansion Space. 

NOW, THEREFORE, in consideration of the foregoing Recitals, which are incorporated herein by this reference, the mutual promises
and conditions contained herein, and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, Landlord and Tenant hereby agree as follows: 

 

	1.	Second Expansion Premises. In addition to the Existing Premises, commencing on the Second Expansion Premises Commencement Date (as defined below),
Landlord leases to Tenant, and Tenant leases from Landlord, the Second Expansion Premises. From and after the Second Expansion Premises Commencement Date, the Existing Premises and the Second Expansion Premises shall be collectively referred to as
the “Premises”. 

  

	2.	Delivery. The “Second Expansion Premises Commencement Date” shall be 1 business day after the mutual execution and delivery of this Third
Amendment by the parties. The “Second Expansion Premises Rent Commencement Date” shall be January 1, 2013. 

 Landlord shall deliver the Second Expansion Premises to Tenant with Landlord’s Work (as defined below) completed on the Second Expansion Premises Commencement Date. Following the Second Expansion
Premises Commencement Date, Tenant shall have the right to construct Tenant Improvements (as defined in the Second Expansion Premises Work Letter attached to this Third Amendment as Exhibit B (“Second EP Work Letter”))
pursuant to the terms of the Second EP Work Letter. 

  
  

			
	1	  	

 Except as set forth in the Lease (including without limitation, Section 13 of
the Lease), as modified by this Third Amendment and the Second EP Work Letter: (i) Tenant shall accept the Second Expansion Premises in their condition as of the Second Expansion Premises Commencement Date, subject to all applicable Legal
Requirements; (ii) Landlord shall not have any obligation to Tenant for any existing defects in the Second Expansion Premises as of the Second Expansion Premises Commencement Date; and (iii) Tenant’s taking possession of the Second
Expansion Premises shall be conclusive evidence that Tenant accepts the Second Expansion Premises in their condition at the time possession was taken. 
 Without limiting Landlord’s repair obligations under Section 13 of the Lease with respect to the entire Premises, for the period of 30 consecutive days after the Second Expansion Premises
Commencement Date, Landlord shall, at its sole cost and expense (which shall not constitute an Operating Expense), be responsible for any repairs that are required to be made to the Building Systems serving the Second Expansion Premises, if the same
were not in good working order as of the Second Expansion Premises Commencement Date. 
 Landlord shall deliver the Second
Expansion Premises to Tenant with the following items (collectively, “Landlord’s Work”) completed: (i) replace any broken, stained or missing ceiling tiles, (ii) patch, repair and spot paint any scuffs or holes in the
walls, (iii) wax VCT flooring if reasonably necessary, (iv) replace any broken light fixtures, and any cracked or broken windows or interior glass, and (v) repair any damage to existing casework such as broken drawers or doors;
provided further, however, that Landlord shall not be required to repair items of normal wear and tear (i.e. surface scratches). 
 Tenant agrees and acknowledges that neither Landlord nor any agent of Landlord has made any representation or warranty with respect to the condition of all or any portion of the Second Expansion Premises,
and/or the suitability of the Second Expansion Premises for the conduct of Tenant’s business, and Tenant waives any implied warranty that the Second Expansion Premises are suitable for the Permitted Use. 

 

	3.	Definition of Premises. Commencing on the Second Expansion Premises Commencement Date, the defined term “Premises” on page 1 of the Lease
is deleted in its entirety and replaced with the following: 

 “Premises: That portion
of the Building containing approximately 36,441 rentable square feet, consisting of (i) a portion of the Building containing approximately 26,299 rentable square feet (the “Original Premises”), (ii) a portion of the
Building containing approximately 1,251 rentable square feet (the “Additional Premises”), and (iii) a portion of the Building containing approximately 8,891 rentable square feet, all as determined by Landlord (“Second
Expansion Premises”), as shown on Exhibit A.” 
 As of the Second Expansion Premises Commencement Date,
Exhibit A to the Lease shall be amended to include the Second Expansion Premises as shown on Exhibit A attached to this Third Amendment. 
  

	4.	Base Term. Commencing on the Second Expansion Premises Commencement Date, the defined term “Base Term” on page 1 of the Lease is deleted
in its entirety and replaced with the following: 

 “Base Term: A term beginning
(i) with respect to the Original Premises, on the Commencement Date, (ii) with respect to the Additional Premises, on the Expansion Premises 

  
  

			
	2	  	

 
Commencement Date, and (iii) with respect to the Second Expansion Premises on the Second Expansion Premises Commencement Date, and ending with respect to the entire Premises on
November 30, 2020.” 
  

	5.	Base Rent. 

 a.
Existing Premises. Tenant shall continue to pay Base Rent for the Existing Premises as provided for in the Lease through the expiration of the Base Term of the Lease. 
 b. Second Expansion Premises. Commencing on the Second Expansion Premises Rent Commencement Date, Tenant shall commence paying Base Rent for the Second Expansion Premises at the same rate per
rentable square foot that Tenant is paying for the Existing Premises, as increased pursuant to the schedule set forth on pages 1 and 2 of the Lease. 
  

	6.	Rentable Area of the Premises. Commencing on the Second Expansion Premises Commencement Date, the defined term “Rentable Area of the
Premises” on page 2 of the Lease is deleted in its entirety and replaced with the following: 

“Rentable Area of the Premises: 36,441 sq. ft.” 

 

	7.	Tenant’s Share. Commencing on the Second Expansion Premises Commencement Date, the defined terms “Tenant’s Share of Operating Expenses
of Building” and “Tenant’s Share of Operating Expenses of Project” on page 2 of the Lease are deleted in their entirety and replaced with the following: 

“Tenant’s Share of Operating Expenses of Building: 72.30% 

Tenant’s Share of Operating Expenses of Project: 24.14%” 

Notwithstanding anything to the contrary contained herein, Tenant shall not be required to pay Operating Expenses with respect to the
Second Expansion Premises for the period commencing on the Second Expansion Premises Commencement Date through December 31, 2012. Tenant shall commencing paying Operating Expenses with respect to the entire Premises on the Second Expansion
Premises Rent Commencement Date. 
  

	8.	Brokers. Landlord and Tenant each represents and warrants that it has not dealt with any broker, agent or other person (collectively,
“Broker”) in connection with the transaction reflected in this Third Amendment and that no Broker brought about this transaction, other than Cassidy Turley BT Commercial and UGL representing the Tenant (collectively,
“Tenant’s Broker”) and Cornish & Carey Commercial/NKF representing the Landlord (“Landlord’s Broker”). Except for the brokerage fees of Tenant’s Broker and Landlord’s Broker, which shall
be paid by Landlord pursuant to a separate written agreement with such Brokers, Landlord and Tenant each hereby agrees to indemnify and hold the other harmless from and against any claims by any Broker claiming a commission or other form of
compensation by virtue of having dealt with Tenant or Landlord, as applicable, with regard to this leasing transaction. 

  

	9.	Miscellaneous. 

 a. This Third Amendment is the entire agreement between the parties with respect to the subject matter hereof and supersedes all prior and contemporaneous oral and written agreements and
discussions. This Third Amendment may be amended only by an agreement in writing, signed by the parties hereto. 

  
  

			
	3	  	

 b. This Third Amendment is binding upon and shall inure to the benefit of the parties
hereto, their respective agents, employees, representatives, officers, directors, divisions, subsidiaries, affiliates, assigns, heirs, successors in interest and shareholders. 
 c. This Third Amendment may be executed in any number of counterparts, each of which shall be deemed an original, but all of which when taken together shall constitute one and the same instrument.
The signature page of any counterpart may be detached therefrom without impairing the legal effect of the signature(s) thereon provided such signature page is attached to any other counterpart identical thereto except having additional signature
pages executed by other parties to this Third Amendment attached thereto. 
 d. Except as amended and/or modified by this
Third Amendment, the Lease is hereby ratified and confirmed and all other terms of the Lease shall remain in full force and effect, unaltered and unchanged by this Third Amendment. In the event of any conflict between the provisions of this Third
Amendment and the provisions of the Lease, the provisions of this Third Amendment shall prevail. Whether or not specifically amended by this Third Amendment, all of the terms and provisions of the Lease are hereby amended to the extent necessary to
give effect to the purpose and intent of this Third Amendment. 
 [Signatures are on next page] 

  
  

			
	4	  	

 IN WITNESS WHEREOF, the parties hereto have executed this Third Amendment as of the
day and year first above written. 
  

			
	TENANT:
	
	 ELAN PHARMACEUTICALS, INC.,
 a Delaware corporation

		
	By:	 	/s/ Alan Campion        
	Its:	 	Treasurer & CFO
	
	LANDLORD:
	
	 ARE-SAN FRANCISCO NO. 33, LLC,
 a Delaware limited liability corporation 

 
							
		
	By:	 	 ALEXANDRIA REAL ESTATE EQUITIES, L.P., a Delaware limited partnership,

managing member

			
		 	By:	 	 ARE-QRS CORP.,
 a
Maryland corporation,
 general partner

				
		 		 	By:	 	/s/ Eric S. Johnson
		 		 	Its:	 	Vice President Real Estate Legal Affairs

  
  

			
	5	  	

 EXHIBIT A 
 Second Expansion Premises 
  
 

 

  
 6 

 

 

  
  

			
	A-2	  	

 EXHIBIT B 
 Second Expansion Premises Work Letter 
 THIS SECOND EXPANSION
PREMISES WORK LETTER dated October 3, 2012 (this “Second Expansion Premises Work Letter”) is made and entered into by and between ARE-SAN FRANCISCO NO. 33, LLC, a Delaware limited liability company
(“Landlord”), and ELAN PHARMACEUTICALS, INC., a Delaware corporation, and is attached to and made a part of that certain Lease Agreement dated as of March 18, 2010, as amended by that certain Letter Agreement dated as of
March 18, 2010, as further amended by that certain First Amendment to Lease dated November 18, 2011, as further amended by that certain Second Amendment to Lease dated as of June 1, 2012, and as further amended by that certain Third
Amendment to Lease dated of even date herewith (as amended, the “Lease”), by and between Landlord and Tenant. Any initially capitalized terms used but not defined herein shall have the meanings given them in the Lease. 

1. General Requirements. 
 (a) Tenant’s Authorized Representative. Tenant designates Rick Smith or Chris Brey (either of them acting individually, a “Tenant’s Representative”) are the only persons
authorized to act for Tenant pursuant to this Second Expansion Premises Work Letter. Landlord shall not be obligated to respond to or act upon any request, approval, inquiry or other communication (“Communication”) from or on behalf
of Tenant in connection with this Second Expansion Premises Work Letter unless such Communication is in writing from a Tenant’s Representative. Tenant may change either Tenant’s Representative at any time upon not less than 5 business days
advance written notice to Landlord. 
 (b) Landlord’s Authorized Representative. Landlord designates Todd Miller,
Catie Paton and Rob Kain (any such individual acting alone, “Landlord’s Representative”) as the only persons authorized to act for Landlord pursuant to this Second Expansion Premises Work Letter. Tenant shall not be obligated
to respond to or act upon any request, approval, inquiry or other Communication from or on behalf of Landlord in connection with this Second Expansion Premises Work Letter unless such Communication is in writing from Landlord’s Representative.
Landlord may change any Landlord’s Representative at any time upon not less than 5 business days advance written notice to Tenant. 
 (c) Architects, Consultants and Contractors. Landlord and Tenant hereby acknowledge and agree that the architect (the “TI Architect”) for the Tenant Improvements (as defined in
Section 2(a) below), the general contractor and any subcontractors for the Tenant Improvements shall be selected by Tenant, subject to Landlord’s approval, which approval shall not be unreasonably withheld, conditioned or delayed.
Landlord shall be named a third party beneficiary of any contract entered into by Tenant with the TI Architect, any consultant, any contractor or any subcontractor, and of any warranty made by any contractor or any subcontractor. 

2. Tenant Improvements. 
 (a) Tenant Improvements Defined. As used herein, “Tenant Improvements” shall mean all improvements to the Second Expansion Premises (and to any other portion of the Premises
reflected in the Space Plans, as approved by Landlord) of a fixed and permanent nature as shown on the TI Construction Drawings, as defined in Section 2(c) below. Other than funding the TI Allowance (as defined below) as provided herein,
Landlord shall not have any obligation whatsoever with respect to the finishing of the Second Expansion Premises for Tenant’s use and occupancy. 
 (b) Tenant’s Space Plans. Tenant shall deliver to Landlord schematic drawings and outline specifications (the “Space Plans”) detailing Tenant’s requirements for the
Tenant Improvements prior to the commencement by Tenant of the construction of the Tenant Improvements. Not more than 15 days thereafter, Landlord shall deliver to Tenant the written objections, questions or comments of Landlord and

  
  

			
	B-1	  	

 
the TI Architect with regard to such Space Plans. Tenant shall cause the Space Plans to be revised to address such written comments and shall resubmit said drawings to Landlord for approval
within 15 days thereafter. Such process shall continue until Landlord has approved the Space Plans for the Tenant Improvements. 

(c) Working Drawings. Not later than 30 days following the approval of the Space Plans by Landlord, Tenant shall cause the TI
Architect to prepare and deliver to Landlord for review and comment construction plans, specifications and drawings for the applicable Tenant Improvements (“TI Construction Drawings”), which TI Construction Drawings shall be
prepared substantially in accordance with the Space Plan. Tenant shall be solely responsible for ensuring that the TI Construction Drawings reflect Tenant’s requirements for such portion of the Tenant Improvements. Landlord shall deliver its
written comments on the TI Construction Drawings to Tenant not later than 10 business days after Landlord’s receipt of the same; provided, however, that Landlord may not disapprove any matter that is consistent with the applicable Space Plan.
Tenant and the TI Architect shall consider all such comments in good faith and shall, within 10 business days after receipt, notify Landlord how Tenant proposes to respond to such comments. Any disputes in connection with such comments shall be
resolved in accordance with Section 2(d) hereof. Provided that the design reflected in the TI Construction Drawings is consistent with the applicable Space Plan, Landlord shall approve the TI Construction Drawings submitted by Tenant.
Once approved by Landlord, subject to the provisions of Section 4 below, Tenant shall not materially modify the Landlord-approved TI Construction Drawings except as may be reasonably required in connection with the issuance of the TI
Permit (as defined in Section 3(a) below). 
 (d) Approval and Completion. If any dispute regarding the
design of any portion of the Tenant Improvements is not settled within 10 business days after notice of such dispute is delivered by one party to the other, Tenant may make the final decision regarding the design of disputed portion of the Tenant
Improvements, provided (i) Tenant acts reasonably and such final decision is either consistent with or a compromise between Landlord’s and Tenant’s positions with respect to such dispute, (ii) that all costs and expenses
resulting from any such decision by Tenant shall be payable out of the TI Allowance (as defined in Section 5(a) below), and (iii) Tenant’s decision will not affect the structural components of the Building or any Building
Systems. Any changes to the TI Construction Drawings following Landlord’s and Tenant’s approval of same requested by Tenant shall be processed as provided in Section 4 hereof. Notwithstanding anything to the contrary contained
herein, Landlord shall have the right to make final decisions, in Landlord’s sole and absolute subjective discretion, with respect to matters concerning the exterior components, site work, façade or other structural components of the
Building or any Building System. 
 3. Performance of the Tenant Improvements. 

(a) Commencement and Permitting of the Tenant Improvements. Tenant shall commence construction of the Tenant Improvements upon
obtaining and delivering to Landlord a building permit (the “TI Permit”) authorizing the construction thereof consistent with the TI Construction Drawings approved by Landlord. The cost of obtaining the TI Permit required for the
Tenant Improvements shall be payable from the TI Allowance. Landlord shall assist Tenant in obtaining such TI Permit(s). Prior to the commencement of any portion of the Tenant Improvements, Tenant shall deliver to Landlord a copy of any contract
with Tenant’s contractors (including the TI Architect), and certificates of insurance from any contractor performing any part of the Tenant Improvement evidencing industry standard commercial general liability, automotive liability,
“builder’s risk”, and workers’ compensation insurance. Tenant shall cause the general contractor to provide a certificate of insurance naming Landlord, Alexandria Real Estate Equities, Inc., and Landlord’s lender (if any) as
additional insureds for the general contractor’s liability coverages required above. 
 (b) Selection of Materials,
Etc. Where more than one type of material or structure is indicated on the TI Construction Drawings approved by Tenant and Landlord, the option will be within Tenant’s reasonable discretion if the matter concerns the Tenant Improvements,
and within Landlord’s sole and absolute subjective discretion if the matter concerns the structural components of the Building or materially affects the operation of, or maintenance requirements associated with, any Building System. 

  
  

			
	B-2	  	

 (c) Tenant Liability. Tenant shall be responsible for correcting any deficiencies or
defects in the Tenant Improvements. 
 (d) Substantial Completion. Tenant shall substantially complete or cause to be
substantially completed the Tenant Improvements in a good and workmanlike manner, in accordance with the TI Permit subject, in each case, to Minor Variations and normal “punch list” items of a non-material nature which do not interfere
with the use of the Second Expansion Premises (“Substantial Completion” or “Substantially Complete”). Upon Substantial Completion of the Tenant Improvements, Tenant shall require the TI Architect and the general
contractor to execute and deliver, for the benefit of Tenant and Landlord, a Certificate of Substantial Completion in the form of the American Institute of Architects (“AIA”) document G704. For purposes of this Second Expansion
Premises Work Letter, “Minor Variations” shall mean any modifications reasonably required: (i) to comply with all applicable Legal Requirements and/or to obtain or to comply with any required permit (including the TI Permit);
(ii) to comport with good design, engineering, and construction practices which are not material; or (iii) to make reasonable adjustments for field deviations or conditions encountered during the construction of the Tenant Improvements.

 4. Changes. Any material changes requested by Tenant to the Tenant Improvements as depicted in any TI Construction
Drawings approved by Landlord, shall be requested and instituted in accordance with the provisions of this Section 4 and shall be subject to the written approval of Landlord, which approval shall not be unreasonably withheld, conditioned
or delayed. 
 (a) Tenant’s Right to Request Changes. If Tenant shall request changes to any Landlord-approved TI
Construction Drawings (“Changes”), Tenant shall request such Changes by notifying Landlord in writing in substantially the same form as the AIA standard change order form (a “Change Request”), which Change Request
shall detail the nature and extent of any such Change. Such Change Request must be signed by Tenant’s Representative. Landlord shall review and approve or disapprove such Change Request within 10 business days thereafter, provided that
Landlord’s approval shall not be unreasonably withheld, conditioned or delayed. 
 (b) Implementation of Changes. If
Landlord approves such Change, Tenant may cause the approved Change to be instituted. If any TI Permit modification or change is required as a result of such Change, Tenant shall promptly provide Landlord with a copy of such TI Permit modification
or change. 
 5. Costs. 
 (a) Budget For Tenant Improvements. Before the commencement of construction of the Tenant Improvements, Tenant shall obtain a detailed breakdown, by trade, of the costs incurred or that will be
incurred, in connection with the design and construction of the Tenant Improvements (the “Budget”) and a schedule for Tenant’s performance and completion of such Tenant Improvements (the “Schedule”), and shall
deliver a copy of each of the Budget and Schedule to Landlord for Landlord’s approval, which shall not be unreasonably withheld or delayed. The Budget shall be based upon the TI Construction Drawings approved by Landlord and shall include a
payment to Landlord of administrative rent (“Administrative Rent”) in the amount of Landlord’s reasonable out-of-pocket costs and expenses associated with Landlord’s engineering and architectural review of the Space Plans
and TI Construction Drawings (and any Changes thereto) for any Tenant Improvements that affect the exterior components, site work, façade or other structural components of the Building or any Building System, all of which shall be payable
from the TI Allowance. 
 (b) TI Allowance. Landlord shall provide to Tenant a tenant improvement allowance
(collectively, the “TI Allowance”) as follows: 

  
  

			
	B-3	  	

 1. a “Tenant Improvement Allowance” in the maximum amount of $20.00 per
rentable square foot in the Second Expansion Premises, which is included in the Base Rent set forth in the Lease; and 
 2. an
“Additional Tenant Improvement Allowance” in the maximum amount of $25.00 per rentable square foot in the office portion of the Second Expansion Premises (consisting of approximately 7,074 rentable square feet), which is included in
the Base Rent set forth in the Lease. 
 The TI Allowance shall be disbursed in accordance with this Work Letter. Tenant shall
have no right to the use or benefit (including any reduction to Base Rent) of any portion of the TI Allowance not required for the construction of (i) the Tenant Improvements described in the TI Construction Drawings approved pursuant to
Section 2(d) or (ii) any Changes pursuant to Section 4. Tenant shall have no right to any portion of the TI Allowance that is not disbursed before November 30, 2015. 

(c) Includable TI Costs. The TI Allowance shall be used solely for the payment of design, permits and construction costs in
connection with the construction of the Tenant Improvements, including, without limitation, the cost of electrical power and other utilities used in connection with the construction of the Tenant Improvements, the cost of preparing the Space Plan
and the TI Construction Drawings, all costs set forth in the Budget, including Landlord’s Administrative Rent, and the cost of Changes (collectively, “TI Costs”). Notwithstanding anything to the contrary contained herein, the
TI Allowance shall not be used to purchase any furniture, personal property or other non-Building system materials or equipment, including, but not limited to, Tenant’s voice or data cabling, non-ducted biological safety cabinets and other
scientific equipment not incorporated into the Tenant Improvements. 
 (d) Excess TI Costs. Landlord shall have no
obligation to bear any portion of the cost of any of the Tenant Improvements except to the extent of the TI Allowance. Notwithstanding anything to the contrary set forth in this Section 5(d), Tenant shall be fully and solely liable for
TI Costs and the cost of Minor Variations in excess of the TI Allowance. 
 (e) Payment for TI Costs. During the course
of design and construction of the Tenant Improvements, Landlord shall reimburse Tenant on a pro rata basis a percentage of the TI Costs (equal to the percentage that the TI Allowance bears to the total Budget, as the same may be amended from time to
time, up to the amount of the TI Allowance actually incurred by Tenant, not more frequently than once a month, against a draw request in Landlord’s standard form, containing evidence of payment of such TI Costs by Tenant and such
certifications, lien waivers (including a conditional lien release for each progress payment and unconditional lien releases for the prior month’s progress payments), inspection reports and other matters as Landlord customarily obtains, to the
extent of Landlord’s approval thereof for payment, no later than 30 days following receipt of such draw request. Upon completion of the construction of the Tenant Improvements (and prior to any final disbursement of the TI Allowance), Tenant
shall deliver to Landlord: (i) sworn statements setting forth the names of all contractors and first tier subcontractors who did the work of the Tenant Improvements, and final, unconditional lien waivers from all such contractors and first tier
subcontractors; (ii) as-built plans (one copy in print format and two copies in electronic CAD format) for such Tenant Improvements; (iii) a certification of substantial completion in Form AIA G704, (iv) a certificate of occupancy for
the Second Expansion Premises; and (v) copies of all operation and maintenance manuals and warranties affecting such Tenant Improvements. 
 6. Miscellaneous. 
 (a) Consents. Whenever consent or approval of
either party is required under this Second Expansion Premises Work Letter, that party shall not unreasonably withhold, condition or delay such consent or approval, except as may be expressly set forth herein to the contrary. 

  
  

			
	B-4	  	

 (b) Modification. No modification, waiver or amendment of this Second Expansion
Premises Work Letter or of any of its conditions or provisions shall be binding upon Landlord or Tenant unless in writing signed by Landlord and Tenant. 

  
  

			
	B-5Assignment of Tenants Interest in Lease and Assumption of Lease Obligations

 Exhibit 10.10 
 ASSIGNMENT OF TENANT’S INTEREST IN LEASE AND 
 ASSUMPTION OF LEASE
OBLIGATIONS 
 (650 Gateway Boulevard, South San Francisco, CA) 

This Assignment of Tenant’s Interest in Lease and Assumption of Lease Obligations (“Agreement”) dated as of
December 2, 2012 is made by and between ELAN PHARMACEUTICALS, INC., a Delaware corporation (“Assignor”), and PROTHENA BIOSCIENCES
INC, a Delaware corporation (“Assignee”). 
 RECITALS

 A. Assignor and ARE-San Francisco No. 33, LLC, a Delaware limited liability company
(“Landlord”), are parties to that certain Lease Agreement dated as of March 18, 2010, as amended by that certain First Amendment to Lease dated as of November 18, 2011, and as further amended by that certain Second
Amendment to Lease dated as of June 1, 2012, and by that certain Third Amendment to Lease dated as of October 3, 2012 (as amended, the “Lease”). Pursuant to the Lease, Assignor, as “Tenant,” leases
certain premises consisting of approximately 36,441 rentable square feet (the “Premises,” as shown on Exhibit A to this Agreement) in a building located at 650 Gateway Boulevard, South San Francisco, California
(“Building”). The Premises are comprised of (i) that certain portion of the Building containing approximately 26,299 rentable square feet (the “Original Premises”), (ii) that certain portion
of the Building containing approximately 1,251 rentable square feet (the “Additional Premises,”), and (iii) that certain portion of the Building consisting of approximately 8,891 rentable square feet (the
“Second Expansion Premises”). Capitalized terms used herein without definition shall have the meanings defined for such terms in the Lease, a true and complete copy of which is attached as Exhibit B to this Agreement.

 B. Assignee requires facilities in the South San Francisco area for its use and occupancy as corporate offices and research
and development facilities. 
 C. Assignee is an entity controlling, controlled by or under common control with Assignor.

 D. Assignor has agreed to assign all of its right, title and interest in the Lease and the Premises to Assignee, on the terms
and conditions hereof, as a Control Permitted Assignment (as such term is defined in Section 22(b) of the Lease). 

E. Assignor desires to assign the Lease and transfer exclusive occupancy and control of the Premises to Assignee, and Assignee desires to
take exclusive possession and occupancy of the Premises from Assignor and assume the Lease, subject to all of the terms and conditions of the Lease and this Agreement. 
 AGREEMENT 
 NOW THEREFORE, for good and valuable consideration, the receipt
and adequacy of which is hereby acknowledged, and in consideration of the foregoing recitals and the provisions set forth below, the parties to this Agreement hereby agree as follows: 

1. Assignment and Assumption. Effective as of the date first set forth above
(the “Effective Date”): (a) Assignor hereby grants, conveys, assigns, releases and transfers to Assignee and Assignee’s legal representatives, heirs, successors and assigns, as a Permitted Assignment, all
of Assignor’s right, title and interest as Tenant in, to and under the Lease, including but not limited to the right to possession of the Premises, along with all of the Assignor’s rights related to the permitted uses of the Premises
(including, without limitation, the permitted uses authorized by that certain Letter Agreement between Landlord and Assignor dated as of March 18, 2010), and all of Assignor’s option rights to expand the Premises and all of Assignor’s
Extension Rights to extend the Term of the Lease (to the extent such rights and options are assignable to Assignee in connection with this Permitted Assignment), to have and to hold the same unto Assignee and Assignee’s legal representatives,
heirs or successors and assigns forever; and (b) Assignee hereby agrees to accept possession of the Premises from Assignor and to assume all of the 

 
rights, obligations and duties of the Tenant under the Lease and agrees, for the benefit of both Assignor and Landlord, to perform and discharge all such obligations and duties of Assignor as
Tenant under the Lease throughout the term of the Lease, as currently scheduled to expire on November 30, 2020 (the “Term”), subject to the Extension Rights to extend the Term of the Lease, which are hereby assigned to
Assignee as part of this Permitted Assignment. Assignor, as of the Effective Date, hereby covenants to deliver exclusive possession and use of the Premises to Assignee (who covenants to accept the Premises and the appurtenant rights, title and
interest pursuant to the assigned leasehold interest in the Premises as hereinafter provided in their current “as is” condition), including, without limitation, all of Assignor’s right, title and interest in and to (subject, however,
to those rights of Landlord set forth in the Lease, if any): (x) all leasehold improvements, fixtures and furnishings in or appurtenant to the Premises (the “Leasehold Improvements”); (y) all of the trade fixtures,
furnishings, equipment and other tangible personal property of the Assignor located in the Premises or elsewhere in the Building or Project to the extent not conveyed by a separate bill of sale or otherwise (the “FF&E”);
and (z) all transferable warranties, guaranties and indemnities, along with any and all transferrable service contracts and maintenance agreements between Assignor and any third party, relating or pertaining to the Premises and/or such
Leasehold Improvements and FF&E, express or implied, and all similar rights which Assignor may have against any manufacturer, supplier, seller, engineer, contractor or builder, in respect of the Premises or the leasehold improvements, fixtures
and furnishings therein (the “Assignable Contract Rights”); provided that Assignor shall have no duty or obligation to enforce such Assignable Contract Rights, which shall be subject to enforcement by Assignee at its sole
cost and expense, and without warranty by, or liability of, Assignor with respect to the enforceability thereof. 
 2. No
Representation regarding Condition of Premises, Building or Project. Assignee specifically acknowledges and agrees that (a) Assignor shall tender, and Assignee shall acquire and accept, possession of the Premises, and any and all Leasehold
Improvements, FF&E and Assignable Contract Rights associated therewith, as of the Effective Date on an “as is with all faults” basis as of such date, and (b) neither Assignor nor any of its officers, directors, employees,
representatives or agents is making any representation or warranty, either express or implied, either directly to Assignee or as a basis for reliance by any Assignor-Indemnified Person (as hereinafter defined, or by Landlord or any other successors
or assigns of the Assignee’s interest in the Premises) regarding the Assignor’s rights, title or interest in the Premises and any and all Leasehold Improvements, FF&E and Assignable Contract Rights, or the physical or legal condition
of any of them, including without limitation: (i) the quality, nature, adequacy and physical condition of the Project, Building or Premises, including, but not limited to, the structural elements, foundation or roof of the Building, and the
electrical, mechanical, HVAC, plumbing, sewage, or utility systems, facilities and appliances of the Project and Building, or the rights of access to or use of the parking facilities of the Project, (ii) the quality, nature, adequacy, and
physical condition of Project soils, geology and any groundwater conditions, (iii) the existence, quality, nature, adequacy and physical condition of utilities serving the Premises, (iv) the use, habitability, merchantability, or fitness,
suitability, value or adequacy of the Project, Building or Premises for any particular purpose, (v) the zoning or other legal status of the Project, Building or Premises or any other public or private restrictions on use of the Premises,
(vi) the compliance of the Project, Building or Premises with any Legal Requirements (including, without limitation, the ADA), (vii) the presence of any Hazardous Materials in, on, under or about the Project, Building or Premises or any
property adjoining or neighboring the Project, (viii) the condition of Assignor’s leasehold title to the Premises, and (ix) the costs and expenses of Assignee’s occupancy or use of the Project, Building and Premises. Assignee:
(I) acknowledges that it has used its independent judgment and made its own determination as to the scope and breadth of its due diligence investigation relative to the legal and physical conditions of the Project, Building and Premises and the
waiver of claims set forth herein; (II) agrees that any and all Claims and Losses (as defined in Section 4 below) incurred or suffered by Assignee or any Assignor-Indemnified Person that arise out of or are caused, or are contributed to,
by (A) any condition of the Premises or any of the Leasehold Improvements, FF&E or Assignable Contract Rights assumed by Assignee, including, without limitation all latent defects and other unknown conditions, or (B) any actual or
alleged representation or warranty made by Assignor or any of its officers, directors, employees, representatives or agents regarding any condition of the Premises or any of the Leasehold Improvements, FF&E or Assignable Contract Rights assumed
by Assignee, whether implied, presumed or expressly provided at law or otherwise, 

  
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arising by virtue of any statute, common law or other legally binding right or remedy in favor of Assignee (except for the certifications made by Assignor pursuant to Section 7 of
this Agreement), are hereby excluded from Assignor’s indemnity obligations under Section 5 of this Agreement (the “Excluded Claims and Losses”), and (III) to the fullest extent permitted by law, hereby
releases Assignor and all Assignee-Indemnified Persons from any and all Excluded Claims and Losses suffered by Assignee and/or any Assignor-Indemnified Person, and assumes the risk of all unknown conditions and unknown and unsuspected Claims and
Losses. Notwithstanding the discovery or existence of any additional or different conditions, claims or facts relative thereto, the Assignee hereby waives the provisions of Section 1542 of the Civil Code of the State of California applicable to
Assignee’s foregoing waivers and its general release of Assignor and all Assignee-Indemnified Persons from Excluded Claims and Losses, which read as follows: 
 A GENERAL RELEASE DOES NOT EXTEND TO CLAIMS WHICH THE CREDITOR DOES NOT KNOW OR SUSPECT TO EXIST IN HIS OR HER FAVOR AT THE TIME OF EXECUTING THE RELEASE, WHICH IF KNOWN BY HIM OR HER MUST HAVE MATERIALLY
AFFECTED HIS OR HER SETTLEMENT WITH THE DEBTOR. 
 3. Covenants. Assignor and Assignee hereby covenant that they shall,
at any time and from time to time, upon written request therefor, execute and deliver to the other party, its successors and assigns, any new or confirmatory instruments which may be reasonably necessary in order to effectuate the assignment and
assumption set forth in Section 1 of this Agreement. Assignor further covenants not to knowingly do or permit to be done anything that would constitute a violation or breach of any of the terms, conditions or provisions of the Lease by
Assignor, if such violation or breach could cause the Lease to be terminated or forfeited by virtue of any rights of termination or forfeiture or any similar remedies reserved by or vested in Landlord, nor shall Assignor exercise any right of
termination of the Lease without the prior written consent of Assignee, which consent may be withheld by Assignee in its sole discretion; provided that no consent of the Assignee shall be required following the occurrence of any Default after the
date of this Agreement (unless such Default is solely attributable to the acts or omissions of Assignor, or unless such Default has been completely and unconditionally waived by Landlord, or Assignee’s cure of such Default has been acknowledged
by Landlord, in writing, with a copy of such written waiver or acknowledgment provided to Assignor). 
 4. Assignee’s
Indemnification of Assignor under the Lease. Assignee shall defend, protect, indemnify, and hold Assignor (and its affiliates, along with the directors, officers, agents and employees of Assignor and its affiliates, collectively with the
Assignor, the “Assignee-Indemnified Persons”) harmless from and against any and all liabilities, obligations, claims, actions, suits or proceedings, and all losses, damages and fines (including those arising from the loss of
life, personal injury and/or property damage, collectively, “Claims and Losses”) and all costs and expenses (including, without limitation, reasonable attorneys’ fees and costs), suffered or incurred by any
Assignee-Indemnified Person and arising, directly or indirectly, from or out of any failure by Assignee to perform Assignee’s obligations under this Agreement, or any breach or alleged breach or violation of any of the Assignee’s
obligations, as Tenant under the Lease or as the tenant in possession of the Premises, in equity or by operation of law (including, without limitation, any holdover occupancy resulting from Assignee’s failure to timely surrender the Premises in
the condition required by the Lease upon the expiration or earlier termination of the Lease Term), or otherwise arising in connection with the Lease or the occupancy or use of the Premises, Building or Project, or the common areas of the Building or
Project, by Assignee or any of its affiliates (or by any assignee, subtenant, licensee or successor to the interests assigned to Assignee pursuant to this Agreement), to the extent occurring or alleged to have occurred from and after the Effective
Date, including, without limitation, the failure of any alterations, repairs or improvements made in or about the Premises after the Effective Date, or made by or for the Assignee to Building or Project, or in the common areas of the Building or
Project (the “Assignee Alterations”) to comply with the applicable requirements of the Lease or any Legal Requirement (including, but not limited to, the ADA), and the cost of removing any leasehold improvements or
alterations (including, without limitation, any Leasehold Improvements), as well as any personal property remaining in the 

  
 3 

 
Premises after the expiration or earlier termination of the Lease (including, without limitation, any FF&E), whether existing or located in the Premises as of the Effective Date or made by or
for Assignee as Assignee Alterations, if such removal is a Landlord requirement of the effective surrender of the Premises, as permitted under the Lease. Assignee hereby covenants and warrants that, in taking possession and control of the Premises
with all Leasehold Improvements, FF&E and any other personal property of the Assignor located therein or about the Building or Project, and in assuming any Assignable Contract Rights, in their “as is” condition, the foregoing
indemnification obligations of the Assignee shall extend to any and all Excluded Claims and Losses (including, without limitation, reasonable attorneys’ fees and costs), suffered or incurred by Assignor or any Assignee-Indemnified Person,
directly or indirectly. 
 5. Assignor’s Indemnification of Assignee under the Lease. Assignor shall defend,
protect, indemnify, and hold Assignee (and its affiliates, along with the directors, officers, agents and employees of Assignee and its affiliates, collectively with the Assignee, the “Assignor-Indemnified Persons”) harmless
from and against any and all Claims and Losses (exclusive of the Excluded Claims and Losses), and all costs and expenses (including, without limitation, reasonable attorneys’ fees and costs), suffered or incurred by any Assignor-Indemnified
Person and arising, directly or indirectly, from or out of any failure by Assignor to perform Assignor’s obligations under this Agreement, or any breach or alleged breach or violation of any of the Assignor’s obligations, as Tenant under
the Lease or as the tenant in possession of the Premises, in equity or by operation of law, to the extent accruing prior to the Effective Date in connection with the Lease or Assignor’s occupancy of the Premises or the Building. 

6. Insurance. Assignee shall also use diligent and prompt efforts following the date of this Agreement to provide Landlord and
Assignor with the certificates of insurance satisfying the requirements of the Lease, and in any event such certificates, showing the information required pursuant to Section 17 of the Lease, including, without limitation, the endorsements
required for the naming of the additional insureds required under the Lease and this Agreement, shall be delivered to Landlord prior to the Effective Date, and to Assignor upon Assignor’s request. Assignee acknowledges and agrees that the
Assignor’s right to carry the commercial general liability insurance coverage required to be maintained by the Tenant pursuant to Section 17 of the Lease (the “Tenant’s CGL Insurance”) in the form of a
claims-made policy (instead of as an occurrence-based policy) is not a right assigned (or assignable) to the Assignee pursuant to this Agreement; and Assignee therefore covenants to Assignor that Assignee shall maintain the Tenant’s CGL
Insurance coverage in the form of an occurrence-based policy. Along with Alexandria Real Estate Equities, Inc., Landlord, and its officers, directors, employees, managers, agents, invitees and contractors, Assignee shall cause the Tenant’s CGL
Insurance policy and the umbrella policy required to be maintained by the Tenant pursuant to Section 17 to be endorsed to name the Assignor as an additional insured; and Assignee shall provide Assignor with certificates of insurance,
showing the limits of coverage required to be maintained by the Tenant under the Lease and showing Assignor as an additional insured, from time to time upon Assignor’s request. Additionally, Assignee covenants to provide Landlord with any and
all notices of cancellation of any of Assignee’s insurance policies required to be maintained pursuant to this Agreement in accordance with those notice requirements set forth in Section 17 of the Lease, and to provide a copy of any
such notice to Assignor contemporaneously with Assignee’s delivery thereof to Landlord. Conditioned upon Assignee’s satisfaction of all of the other insurance obligations of the Tenant set forth in the Lease, the insurance policies
maintained by Assignee shall provide primary coverage (as between Sublessee and Tenant) to Landlord under the Lease, Assignor and Assignee each hereby releases the other and waives its respective rights of recovery against the other for direct or
consequential loss or damage arising out of or incident to the perils covered by property insurance carried by such party to the extent of such insurance and waive any right of subrogation which might otherwise exist in or accrue to any person on
account thereof. 
 7. Certifications of Assignor. 

(a) Assignor hereby certifies to Assignee the following information with respect to the Lease and agrees that Assignee may rely upon the
same: 
 (i) The Lease is in full force and effect and has not been modified or amended, except pursuant to
written amendments or modifications previously provided by Assignor to Assignee; 

  
 4 

 (ii) To the best of Assignor’s knowledge and belief, there is no
default by Landlord under the Lease and no event has occurred that, with the passage of time or the giving of notice, or both, would constitute a default by Landlord under the Lease; and 

(iii) Assignor has not entered into any sublease, assignment or any other agreement transferring any of its interest in
the Lease or the premises subject to the Lease prior to the date of this Agreement. 
 (b) Assignor hereby certifies to Landlord
that the Assignee is an entity controlled by, controlling or under common control with Assignor as required for the assignment of the Lease pursuant to this Agreement to qualify as a Control Permitted Assignment in accordance with the terms and
conditions of such a Permitted Assignment as are set forth in Section 22 of the Lease, and agrees that Landlord may rely upon such certification. 
 8. Authority. Each party represents and warrants to the other that it has full power and authority to execute and fully perform its obligations under this Agreement (and Assignee further represents
and warrants that it has full power and authority to fully perform its obligations under the Lease) pursuant to its governing instruments, without the need for any further action, and that the person(s) executing this Agreement on behalf of such
party are duly designated agents and are authorized to do so. 
 9. Notices. From and after the Effective Date, notices
to the Assignor and Assignee under the Lease shall be addressed, respectively, to: 
 Assignor: 

180 Oyster Point 

South San Francisco, CA 94080 
 Attention: Mr. Rick Smith 
 With a copy to: 

180 Oyster Point 

South San Francisco, CA 94080 
 Attention: Vice President, Corporate Legal 
 Assignee: 

650 Gateway Boulevard, Suite 100 
 South San Francisco, CA 94080 
 Attn: Chief Financial Officer 

10. Counterparts. This Agreement may be executed in any number of counterparts, each of which shall be a valid and binding
original, but all of which, taken together, shall constitute one and the same instrument. 
 11. No Modification of Lease;
Limitations on Further Assignments. There shall be no further assignment of the Lease, nor any subletting of all or any portion of the Premises demised under the Lease, except in accordance with the terms and conditions of the Lease; and nothing
contained herein shall be construed to modify, waive, impair, or affect any of the terms, covenants or conditions contained in Section 22 of the Lease, including, without limitation, Landlord’s rights thereunder. Without limiting
the foregoing, as between Assignor and Assignee with respect to any proposed subletting of all or any portion of the Premises or assignment of the Lease by Assignee: (a) to the extent that the consent of Landlord to such assignment or
subletting is required pursuant to Section 22 of the Lease, Assignee shall request both 

  
 5 

 
Landlord’s and Assignor’s consent to such further assignment or subletting; and (b) Assignor’s rights with respect to any such request by Assignee for Assignor’s consent
to any further assignment or subletting by Assignee shall be the rights of Landlord under Section 22 of the Lease. 

12. Binding Effect. This Agreement will be binding upon and inure to the benefit of the successors and assigns of each party.

 13. Governing Law. This Agreement shall in all respects be construed in accordance with and governed by the laws of
the State of California without giving effect to its conflicts-of-laws principles. 
 IN WITNESS WHEREOF, the parties have
executed this Assignment of Tenant’s Interest in Lease and Assumption of Lease Obligations as of the date first set forth above. 
  

											
		 	ASSIGNOR	 	ASSIGNEE
			
		 	 Elan Pharmaceuticals, Inc.
 a Delaware corporation
	 	 Prothena Biosciences Inc
 a Delaware corporation

						
		 	By:	 	 /s/ John L. Donahue
	 		 	By:	 	 /s/ John Randall Fawcett

						
		 	Name:	 	John L. Donahue	 		 	Name:	 	John Randall Fawcett
						
		 	Title:	 	Secretary	 		 	Title:	 	Chief Financial Officer and Treasurer

  
 6 

 EXHIBIT A 
 PREMISES 

  
 A-1

 EXHIBIT B 
 LEASE 

  
 A-2

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