9LHF | pdb_00009lhf

Crystal structure of A13 with hGSTO1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.248 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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Literature

Discovery of Potent, Allosteric GSTO1 Covalent Inhibitors with a New Binding Mode.

Sun, Y.Zhang, F.Zhou, L.Feng, Y.Yang, S.Lu, Q.Yuan, X.Hou, W.Liu, B.Guo, Z.Chen, L.Peng, B.Yin, X.Zhang, Y.Yang, J.Chen, N.Lu, W.

(2025) J Med Chem 68: 24075-24093

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01724
  • Primary Citation of Related Structures:  
    9LHF

  • PubMed Abstract: 

    GSTO1 activates the NLRP3 inflammasome by deglutathionylating NEK7 at Cys253, driving proinflammatory responses. Using PRM-based targeted mass spectrometry, we identified compound A1 as a covalent GSTO1 inhibitor modifying Cys32. Ligand-based optimization generated analogues with diverse activities; among them, A13 exhibited moderate target engagement ( k inact / K I = 226 M -1 ·s -1 ), excellent cysteine selectivity confirmed by desthiobiotin iodoacetamide (DBIA)- and alkyne-based ABPP, and superior metabolic stability in human liver microsomes. High-resolution crystal structures revealed an unexpected A13 binding mode occupying a new hydrophobic pocket distinct from known GSTO1 inhibitors. Functionally, covalent targeting of GSTO1-C32 by A13 markedly reduced LPS-induced IL-1β and IL-18 secretion in human monocyte-derived macrophages. Collectively, these results identify A13 as a potent, selective, and metabolically stable lead compound for developing next-generation GSTO1 inhibitors targeting inflammatory diseases.


  • Organizational Affiliation
    • Lingang Laboratory, Shanghai 200031, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase omega-1
A, B
245Homo sapiensMutation(s): 0 
Gene Names: GSTO1GSTTLP28
EC: 2.5.1.18 (PDB Primary Data), 1.8.5.1 (PDB Primary Data), 1.20.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P78417 (Homo sapiens)
Explore P78417 
Go to UniProtKB:  P78417
PHAROS:  P78417
GTEx:  ENSG00000148834 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78417
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ELW (Subject of Investigation/LOI)
Query on A1ELW

Download Ideal Coordinates CCD File 
C [auth A]1-[(2~{R})-2-[5-[4-(trifluoromethyl)phenyl]-1,3,4-thiadiazol-2-yl]pyrrolidin-1-yl]propan-1-one
C16 H16 F3 N3 O S
LLGURZQPWOPEMU-GFCCVEGCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.248 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.958α = 90
b = 68.277β = 112.59
c = 62.757γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
autoPXdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Database references