Exhibit 10.1

THIRD AMENDMENT TO LEASE

THIS THIRD AMENDMENT TO LEASE (this “Amendment”) is entered into as of this 30th
day of July, 2018 (the “Third Amendment Execution Date”), by and between
BMR-3545-3575 JOHN HOPKINS LP, a Delaware limited partnership (“Landlord,” as
successor-in-interest to BMR-John Hopkins Court LLC), and ATYR PHARMA, INC., a
Delaware corporation (“Tenant”).

RECITALS

A.WHEREAS, Landlord and Tenant are parties to that certain Lease dated as of
December 22, 2011, as amended by that certain First Amendment to Lease dated as
of January 4, 2017, and as further amended by that certain Second Amendment to
Lease dated as of April 27, 2017 (the “Second Amendment”) (collectively, and as
the same may have been further amended, amended and restated, supplemented or
modified from time to time, the “Existing Lease”), whereby Tenant leases certain
premises (the “Existing Premises”) from Landlord at 3545-3575 John Hopkins Court
in San Diego, California (the “Building”);

B.WHEREAS, Tenant wishes to surrender a portion of the Existing Premises to
Landlord and extend the Term of the Existing Lease; and

C.WHEREAS, Landlord and Tenant desire to modify and amend the Existing Lease
only in the respects and on the conditions hereinafter stated.

AGREEMENT

NOW, THEREFORE, Landlord and Tenant, in consideration of the mutual promises
contained herein and for other good and valuable consideration, the receipt and
sufficiency of which are hereby acknowledged, and intending to be legally bound,
agree as follows:

1.Definitions.  For purposes of this Amendment, capitalized terms shall have the
meanings ascribed to them in the Existing Lease unless otherwise defined
herein.  The Existing Lease, as amended by this Amendment, is referred to
collectively herein as the “Lease.” From and after the date hereof, the term
“Lease,” as used in the Existing Lease, shall mean the Existing Lease, as
amended by this Amendment.

2.Correction to Exhibit A of Second Amendment.  Exhibit A of the Second
Amendment, depicting the Expansion Premises (as defined in the Second
Amendment), is hereby deleted in its entirety and replaced with Exhibit A
attached hereto.  This replacement shall be deemed effective as of the Second
Amendment Execution Date.  

3.Reduction of Premises.  Effective as of the Partial Surrender Effective Date
(as defined below), the Existing Premises shall be modified to exclude that
certain portion containing approximately three thousand nine hundred eighty-six
(3,986) square feet of Rentable Area located on the first (1st) floor of the
Building (as more particularly described on Exhibit B attached hereto,
the “Surrender Premises”).  From and after the Partial Surrender Effective Date,
the term

BioMed Realty form dated 9/28/17

--------------------------------------------------------------------------------

 

“Premises” as used in the Lease shall mean the remaining twenty thousand five
hundred eight (20,508) square feet of Rentable Area at the Building.

4.Partial Surrender Effective Date.  The Partial Surrender Effective Date shall
be the date that is the later of: (a) the Third Amendment Execution Date, and
(b) the day immediately following the date Tenant surrenders the Surrender
Premises in accordance with all of the terms, conditions and provisions of the
Existing Lease.  Tenant shall execute and deliver to Landlord written
acknowledgment of the actual Partial Surrender Effective Date and the Term
Expiration Date within ten (10) days thereof, in the form attached as Exhibit C
hereto.  Failure to execute and deliver such acknowledgment, however, shall not
affect the Partial Surrender Effective Date or Landlord’s or Tenant’s liability
hereunder.  For the avoidance of doubt, the IT Space License granted to Tenant
pursuant to Section 6 of the Second Amendment shall remain in full force and
effect through the Extension Term Expiration Date; provided, however, that
Tenant shall remove its IT Equipment from its current rack location in the IT
Space and install a new IT rack in the IT Space in accordance with the
provisions of Section 6.6 of the Second Amendment.  

5.Condition of Premises.  Tenant acknowledges that (a) it is in possession of
and is fully familiar with the condition of the Premises and, notwithstanding
anything to the contrary in the Lease, agrees to take the same in its condition
“as is” as of the Partial Surrender Effective Date, (b) neither Landlord nor any
agent of Landlord has made (and neither Landlord nor any agent of Landlord
hereby makes) any representation or warranty of any kind whatsoever, express or
implied, regarding the Premises, including (without limitation) any
representation or warranty with respect to the condition of the Premises or with
respect to the suitability of the Premises for the conduct of Tenant’s business
and (c) Landlord shall have no obligation to alter, repair or otherwise prepare
the Premises for Tenant’s occupancy or to pay for any improvements to the
Premises.  The Premises has not undergone inspection by a Certified Access
Specialist (as defined in California Civil Code Section 55.52).  Tenant’s
continued possession of the Premises shall, except as otherwise agreed to in
writing by Landlord and Tenant, conclusively establish that the Premises were at
such time in good, sanitary and satisfactory condition and repair.

6.Furniture.  Ownership of existing furniture and network cabling in Surrender
Premises, as itemized in Exhibit D attached to this Amendment, shall be
transferred to Landlord in its as-is condition as of the Partial Surrender
Effective Date.

7.Extension Term.  Notwithstanding anything to the contrary set forth herein,
the Term is hereby extended by forty-eight (48) months and the Term Expiration
Date is hereby amended to be May 15, 2023.  The period of time from the Partial
Surrender Effective Date through the new Term Expiration Date shall be referred
to herein as the “Extension Term” and any references to “Term” in the Lease
shall be deemed to include the Extension Term.  Notwithstanding anything to the
contrary set forth in the Existing Lease, the Option to extend the Term of the
Lease as set forth in Section 42 of the Existing Lease shall terminate as of the
Third Amendment Execution Date, and Tenant shall have no further options to
extend the Lease.  

8.Base Rent.  Notwithstanding anything to the contrary in the Existing Lease,
commencing as of the Partial Surrender Effective Date and continuing throughout
the remainder

2

 

--------------------------------------------------------------------------------

 

of the Term, Base Rent for the Premises shall be as set forth in the table
below, subject to the full abatement of Base Rent from January 1, 2019 until
February 28, 2019.

Dates

Square Feet of Rentable Area

Base Rent per Square Foot of Rentable Area

Monthly Base Rent

Annual Base Rent

Partial Surrender Effective Date –

Day Before 1st Anniversary of Partial Surrender Effective Date*

20,508

$3.90 monthly

$79,981.20

$959,774.40

1st Anniversary of Partial Surrender Effective Date –

Day Before 2nd Anniversary of Partial Surrender Effective Date

20,508

$4.02 monthly

$82,442.16

$989,305.92

2nd Anniversary of Partial Surrender Effective Date –

Day Before 3rd Anniversary of Partial Surrender Effective Date

20,508

$4.14 monthly

$84,903.12

$1,018,837.44

3rd Anniversary of Partial Surrender Effective Date –

Day Before 4th Anniversary of Partial Surrender Effective Date

20,508

$4.26 monthly

$87,364.08

$1,048,368.96

4th Anniversary of Partial Surrender Effective Date –

5/15/2023

20,508

$4.39 monthly

$90,030.12

$1,080,361.44

*Subject to the Base Rent abatement set forth in Section 8 hereof.

 

9.Tenant’s Pro Rata Share.  From and after the Expansion Space Commencement
Date, Tenant’s Pro Rata Share shall equal 28.41%.

 

3

 

--------------------------------------------------------------------------------

 

10.Additional Insureds.  The first sentence of Section 23.4 of the Existing
Lease is hereby deleted in its entirety and replaced with the following:

 

“23.4The insurance required to be purchased and maintained by Tenant pursuant to
this Lease shall name Landlord, BioMed Realty LLC, BioMed Realty, L.P., BRE
Edison L.P., BRE Edison LLC, BRE Edison Holdings L.P., BRE Edison Holdings LLC,
BRE Edison Parent L.P. and their respective officers, employees, agents, general
partners, members, subsidiaries, affiliates and Lenders (“Landlord Parties”) as
additional insureds.”

 

11.Broker. Tenant represents and warrants that it has not dealt with any broker
or agent in the negotiation for or the obtaining of this Amendment, other than
Hughes Marino (“Tenant Broker”) and Jones Lang LaSalle (“Landlord Broker”), and
agrees to reimburse, indemnify, save, defend (at Landlord’s option and with
counsel reasonably acceptable to Landlord, at Tenant’s sole cost and expense)
and hold harmless the Landlord Indemnitees for, from and against any and all
cost or liability for compensation claimed by any such broker or agent, other
than Tenant Broker and Landlord Broker, employed or engaged by it or claiming to
have been employed or engaged by it.  Each of Tenant Broker and Landlord Broker
are entitled to a leasing commission in connection with the making of this
Amendment, and Landlord shall pay such commissions pursuant to separate
agreements.

 

12.No Default.  Tenant represents, warrants and covenants that, to the best of
Tenant’s knowledge, Landlord and Tenant are not in default of any of their
respective obligations under the Existing Lease and no event has occurred that,
with the passage of time or the giving of notice (or both) would constitute a
default by either Landlord or Tenant thereunder.

13.Notices.  Tenant confirms that, notwithstanding anything in the Lease to the
contrary, notices delivered to Tenant pursuant to the Lease should be sent to:

aTyr Pharma, Inc.

3545 John Hopkins Court

San Diego, California 92121

Attn: Chief Financial Officer

 

14.Effect of Amendment.  Except as modified by this Amendment, the Existing
Lease and all the covenants, agreements, terms, provisions and conditions
thereof shall remain in full force and effect and are hereby ratified and
affirmed.  In the event of any conflict between the terms contained in this
Amendment and the Existing Lease, the terms herein contained shall supersede and
control the obligations and liabilities of the parties.

15.Successors and Assigns.  Each of the covenants, conditions and agreements
contained in this Amendment shall inure to the benefit of and shall apply to and
be binding upon the parties hereto and their respective heirs, legatees,
devisees, executors, administrators and permitted successors and assigns and
sublessees.  Nothing in this section shall in any way alter the provisions of
the Lease restricting assignment or subletting.

4

 

--------------------------------------------------------------------------------

 

16.Miscellaneous.  This Amendment becomes effective only upon execution and
delivery hereof by Landlord and Tenant. The captions of the paragraphs and
subparagraphs in this Amendment are inserted and included solely for convenience
and shall not be considered or given any effect in construing the provisions
hereof.  All exhibits hereto are incorporated herein by reference.  Submission
of this instrument for examination or signature by Tenant does not constitute a
reservation of or option for a lease, and shall not be effective as a lease,
lease amendment or otherwise until execution by and delivery to both Landlord
and Tenant.

17.Authority.  Tenant guarantees, warrants and represents that the individual or
individuals signing this Amendment have the power, authority and legal capacity
to sign this Amendment on behalf of and to bind all entities, corporations,
partnerships, limited liability companies, joint venturers or other
organizations and entities on whose behalf such individual or individuals have
signed.  Landlord guarantees, warrants and represents that the individual or
individuals signing this Amendment on behalf of Landlord have the power,
authority and legal capacity to sign this Amendment on behalf of and to bind all
entities, corporations, partnerships, limited liability companies, joint
venturers or other organizations and entities on whose behalf such individual or
individuals have signed.

18.Counterparts; Facsimile and PDF Signatures.  This Amendment may be executed
in one or more counterparts, each of which, when taken together, shall
constitute one and the same document.  A facsimile or portable document format
(PDF) signature on this Amendment shall be equivalent to, and have the same
force and effect as, an original signature.

[REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK]

5

 

--------------------------------------------------------------------------------

 

IN WITNESS WHEREOF, Landlord and Tenant have executed this Amendment as of the
date and year first above written.

LANDLORD:

BMR-3545-3575 JOHN HOPKINS LP,

a Delaware limited partnership

By:

/s/ Marie Lewis

Name:

Marie Lewis

Title:

Vice President, Legal

 

TENANT:

ATYR PHARMA, INC.,

a Delaware corporation

By:

/s/ Nancy Denyes Krueger

Name:

Nancy Denyes Krueger

Title:

Vice President, Legal Affairs

 

 

 

 

--------------------------------------------------------------------------------

 

EXHIBIT A

EXPANSION SPACE

[goclowb2ukgu000001.jpg]

 

 

A-1

--------------------------------------------------------------------------------

 

EXHIBIT B

SURRENDER PREMISES

 

[goclowb2ukgu000002.jpg]

 

 

 

 

B-1

--------------------------------------------------------------------------------

 

EXHIBIT C

ACKNOWLEDGEMENT OF PARTIAL SURRENDER EFFECTIVE DATE

AND TERM EXPIRATION DATE

This acknowledgement of PARTIAL SURRENDER EFFECTIVE date and TERM EXPIRATION
DATE is entered into as of [_______], 20[__], with reference to that certain
Lease dated as of December 22, 2011 (as amended, the “Lease”), by aTyr Pharma,
Inc., a Delaware corporation (“Tenant”), in favor of BMR-3545-3575 John Hopkins
LP, a Delaware limited partnership (“Landlord”, as successor-in-interest to
BMR-John Hopkins Court LLC).  All capitalized terms used herein without
definition shall have the meanings ascribed to them in the Lease.

Tenant hereby confirms the following:

1.Tenant surrendered the Surrender Premises on [_______], 20[___].

2.All conditions of the Lease to be performed by Landlord as a condition to the
full effectiveness of the Lease have been satisfied, and Landlord has fulfilled
all of its duties in the nature of inducements offered to Tenant to lease the
Premises.

3.In accordance with the provisions of Section 3 of the Third Amendment to
Lease, the Partial Surrender Effective Date is [_______], 20[__], and, unless
the Lease is terminated prior to the Term Expiration Date pursuant to its terms,
the Term Expiration Date shall be [_______], 20[__].

4.The Lease is in full force and effect, and the same represents the entire
agreement between Landlord and Tenant concerning the Premises [, except
[_______]].

5.Tenant has no existing defenses against the enforcement of the Lease by
Landlord, and there exist no offsets or credits against Rent owed or to be owed
by Tenant.

6.The obligation to pay Rent is presently in effect and all Rent obligations on
the part of Tenant under the Lease with respect to the Premises commenced to
accrue on [_______], 20[__], with Base Rent payable on the dates and amounts set
forth in the chart below:

 

Dates

Approximate Square Feet of Rentable Area

Base Rent per Square Foot of Rentable Area

Monthly Base Rent

Annual Base Rent

___/___/___ - ___/___/___*

20,508

$3.90 monthly

$79,981.20

$959,774.40

C-1

 

--------------------------------------------------------------------------------

 

___/___/___ - ___/___/___

20,508

$4.02 monthly

$82,442.16

$989,305.92

___/___/___ - ___/___/___

20,508

$4.14 monthly

$84,903.12

$1,018,837.44

___/___/___ - ___/___/___

20,508

$4.26 monthly

$87,364.08

$1,048,368.96

___/___/___ - 5/15/2023

20,508

$4.39 monthly

$90,030.12

$1,080,361.44

*Subject to the full abatement of Base Rent from January 1, 2019 until February
28, 2019.

7.The undersigned Tenant has not made any prior assignment, transfer,
hypothecation or pledge of the Lease or of the rents thereunder or sublease of
the Premises or any portion thereof.

[REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK]

C-2

 

--------------------------------------------------------------------------------

 

IN WITNESS WHEREOF, Tenant has executed this Acknowledgment of Partial Surrender
Effective Date and Term Expiration Date as of the date first written above.

 

TENANT:

 

aTyr Pharma, Inc.,

a Delaware corporation

 

 

 

By:

Name:

Title:

C-3

--------------------------------------------------------------------------------

 

EXHIBIT D

INVENTORY OF FURNITURE AND NETWORK CABLING
IN SURRENDER PREMISES

Office Cubicles:  

16

Desks:

  2

Chairs:

26

Tables:

  5

File Cabinets:

  3

Network cabling in Surrender Premises

 

D-1