9X2K | pdb_00009x2k

AARS1 bound with XY353 and Gly-SA

• PDB DOI: https://doi.org/10.2210/pdb9X2K/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-10-05 Released: 2026-08-05 
• Deposition Author(s): Huang, Y., Liu, S., Min, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.218 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Covalent allosteric inhibition of AARS1 lactyltransferase.

Huang, Y., Liu, S., Tian, L., Tang, Y., Dou, Y., Wang, H., Zheng, T., Wang, M., Li, R., Wang, Z., Zhou, Z., Chen, X., Min, J.

(2026) Nat Commun 17

• PubMed: 42744818 
• DOI: https://doi.org/10.1038/s41467-026-76732-9
• Primary Citation Related Structures: 
  9X2H, 9X2I, 9X2J, 9X2K


• PubMed Abstract: 
  

  Alanyl-tRNA synthetase 1 (AARS1) was recently identified as a lactyltransferase responsible for protein lactylation, a modification associated with epigenetic regulation and metabolic adaptation. Here, we report compound XY353, which covalently binds C184 of AARS1, inducing steric clashes with F175 and triggering structural rearrangements in the region that displace W176, a key residue for lactate binding. By means of a combination of a variety of biophysical and enzymatic assays with MD simulations and structural analysis, we show that XY353 and its derivative XY353-1 inhibit AARS1 by competing with lactate via the C184-F175-W176 relay, supporting a covalent allosteric mechanism of inhibition, which is further confirmed by our cellular data that XY353-1 reduces lactylation of the AARS1 substrate YAP and suppresses the proliferation of HGC-27 cells. Collectively, these findings identify a covalent allosteric mechanism for AARS1 inhibition and provide chemical tools to explore its biological functions.

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Organizational Affiliation: 
• Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China. [e-mail].
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, School of Life Sciences, Central China Normal University, Wuhan, China. [e-mail].
Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China.
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, School of Life Sciences, Central China Normal University, Wuhan, China.
Department of Medical Ultrasound, Tongji University Affiliated Tenth People's Hospital, Shanghai, China.
National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China.
State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Pharmacy, Jinan University, Guangzhou, China.
State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.
State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Pharmacy, Jinan University, Guangzhou, China. [e-mail].
Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China. [e-mail].
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, School of Life Sciences, Central China Normal University, Wuhan, China. [e-mail].
Department of Physiology, University of Toronto, Toronto, ON, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.88 kDa 
• Atom Count: 3,300 
• Modeled Residue Count: 378 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine--tRNA ligase, cytoplasmic	A	384	Homo sapiens	Mutation(s): 0  Gene Names: AARS1, AARS EC: 6.1.1.7 (PDB Primary Data), 6 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49588 (Homo sapiens) Explore P49588  Go to UniProtKB:  P49588
PHAROS:  P49588 GTEx:  ENSG00000090861

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G5A	B [auth A]	5'-O-(glycylsulfamoyl)adenosine C12 H17 N7 O7 S AMWPZASLDLLQFT-JJNLEZRASA-N
A1EYX (Subject of Investigation/LOI)	C [auth A]	~{N}-(5-chloranyl-1,3-thiazol-2-yl)ethanamide C5 H5 Cl N2 O S YLRXYIGXXMJPOP-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.218 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.686	α = 90
b = 67.105	β = 127.63
c = 75.468	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-05 
Deposition Author(s): Huang, Y., Liu, S., Min, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82404418

Revision History  

• Version 1.0: 2026-08-05
  Type: Initial release
  
• Version 1.1: 2026-09-23
  Changes: Database references
• Version 1.2: 2026-09-30
  Changes: Database references