Human Glyoxalase I with an N-hydroxypyridone inhibitor

Experimental Data Snapshot

  • Resolution: 1.47 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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Design and evaluation of azaindole-substituted N-hydroxypyridones as glyoxalase I inhibitors

Chiba, T.Ohwada, J.Sakamoto, H.Kobayashi, T.Fukami, T.A.Irie, M.Miura, T.Ohara, K.Koyano, H.

(2012) Bioorg Med Chem Lett 22: 7486-7489

  • DOI: https://doi.org/10.1016/j.bmcl.2012.10.045
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We conducted a high throughput screening for glyoxalase I (GLO1) inhibitors and identified 4,6-diphenyl-N-hydroxypyridone as a lead compound. Using a binding model of the lead and public X-ray coordinates of GLO1 enzymes complexed with glutathione analogues, we designed 4-(7-azaindole)-substituted 6-phenyl-N-hydroxypyridones. 7-Azaindole's 7-nitrogen was expected to interact with a water network, resulting in an interaction with the protein. We validated this inhibitor design by comparing its structure-activity relationship (SAR) with that of corresponding indole derivatives, by analyzing the binding mode with X-ray crystallography and by evaluating its thermodynamic binding parameters.

  • Organizational Affiliation

    Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara Kamakura, Kanagawa 247-8530, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lactoylglutathione lyase
A, B
187Homo sapiensMutation(s): 0 
Gene Names: GLO1
UniProt & NIH Common Fund Data Resources
Find proteins for Q04760 (Homo sapiens)
Explore Q04760 
Go to UniProtKB:  Q04760
PHAROS:  Q04760
GTEx:  ENSG00000124767 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04760
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
HPJ BindingDB:  3VW9 Ki: 11 (nM) from 1 assay(s)
IC50: 11 (nM) from 1 assay(s)
Binding MOAD:  3VW9 IC50: 11 (nM) from 1 assay(s)
PDBBind:  3VW9 IC50: 11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.47 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.99α = 90
b = 66.98β = 90
c = 68.53γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description