4X2A

Crystal structure of mouse glyoxalase I complexed with baicalein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

In Vitro Inhibition of Glyoxalase І by Flavonoids: New Insights from Crystallographic Analysis.

Zhang, H.Zhai, J.Zhang, L.Li, C.Zhao, Y.Chen, Y.Li, Q.Hu, X.P.

(2016) Curr Top Med Chem 16: 460-466

  • DOI: https://doi.org/10.2174/1568026615666150813150944
  • Primary Citation of Related Structures:  
    4X2A

  • PubMed Abstract: 

    The antitumor pharmacological property of flavonoids is correlated with inhibition towards glyoxalase I (GLOI), a critical zinc-enzyme in the methylglyoxal detoxification pathway. In this study, 16 flavonoids were examined, and only baicalein (Ki of 0.183 µM) is identified as a potent in vitro GLOI inhibitor. X-ray crystallographic analysis reveals that baicalein chelates with the catalytic Zn(2+) via its characteristic C6/C7 hydroxyl groups. The coordination ability of flavonoids, and therefore their ability to inhibit GLOI, is determined by the Zn(2+) coordination geometry, the rigid skeleton of flavonoids and the geometry of the hydrophobic cavity of the GLOI active site. This structural basis could be useful in predicting GLOI inhibition of other natural polyphenols.


  • Organizational Affiliation

    School of Pharmaceutical Sciences & Centre for Cellular and Structural Biology of Sun Yat-sen University, Guangzhou 510006, P.R. China. huxpeng@mail.sysu.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lactoylglutathione lyase
A, B
184Mus musculusMutation(s): 0 
Gene Names: Glo1
EC: 4.4.1.5
UniProt
Find proteins for Q9CPU0 (Mus musculus)
Explore Q9CPU0 
Go to UniProtKB:  Q9CPU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CPU0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
3WL BindingDB:  4X2A IC50: 1.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.501α = 90
b = 64.502β = 104.79
c = 63.152γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-10-28
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-29
    Changes: Database references