Commitments and Contingencies

9 Months Ended

Sep. 30, 2025

Commitments and Contingencies Disclosure [Abstract]

4. Commitments and Contingencies

Operating Leases

Corporate Headquarters Facility Lease

In May 2022, we entered into a non-cancelable facility lease that is subject to base lease payments that started at $5.75 per square foot of rentable area per month for the first 12 months of the lease and which escalate 3.0% annually over the term of the lease, and additional charges for common area maintenance and other costs. The term of the lease (the Lease Term) commenced on March 20, 2023 (the Lease Commencement Date) and will continue for 124 months from the Lease Commencement Date. We also have one option to extend the Lease Term for five years. In April 2024, we entered into a lease amendment for additional common area amenities, effective as of June 2023. The amendment increased the total rentable square feet from 23,696 rentable square feet to 24,866 rentable square feet. We provided a $0.7 million security deposit in the form of a letter of credit which is included in restricted cash as of September 30, 2025.

Future minimum payments under the facility lease and a reconciliation to the operating lease liability as of September 30, 2025 were as follows (in thousands):


	Operating Leases
2025	$	434
2026		1,780
2027		1,916
2028		1,975
2029 and thereafter		9,837
Less: Amount representing interest		(4,611	)
Present value of lease payments		11,331
Less: Current portion of operating lease liability		(799	)
Long-term operating lease liability, net of current portion	$	10,532

For each of the three months ended September 30, 2025 and 2024, we recorded an operating lease expense of $0.4 million. For the nine months ended September 30, 2025 and 2024, we recorded an operating lease expense of $1.2 million and $1.1 million, respectively. As of September 30, 2025, the weighted-average remaining lease term was 7.8 years and the weighted average discount rate was 8.8%.

Financing Leases

In April 2022, we entered into a master financing lease agreement to lease various research and development and information technology equipment over a 48-month term. Future minimum payments under the financing lease and reconciliation to the financing lease liability as of September 30, 2025 were as follows (in thousands):


	Financing Leases
2025	$	158
2026		676
2027		264
Less: Amount representing interest		(70	)
Present value of lease payments		1,028
Less: Current portion of financing lease liability		(630	)
Long-term financing lease liability, net of current portion	$	398

As of September 30, 2025, the weighted-average remaining lease term was 1.3 years and the weighted-average discount rate was 8.4%. As of September 30, 2025, we have a $1.5 million deposit held as collateral for the leased equipment, and this deposit is included in restricted cash.

Litigation

On October 9, 2025 and October 22, 2025, two substantially similar putative securities class action complaints were filed in the U.S. District Court for the Southern District of California, naming aTyr Pharma, Inc. and our Chief Executive Officer, Sanjay Shukla. The complaints allege certain violations of the U.S. federal securities laws and seek unspecific damages.

We make provisions for liabilities when they are both probable that a liability has been incurred and the amount can be reasonably estimated. No such liability has been recorded related to this matter. With regard to legal fees, such as attorney fees related to this matter or any other legal matters, we recognize such costs as incurred.

aTYR PHARMA INC 10-Q