4X2A

Crystal structure of mouse glyoxalase I complexed with baicalein

• PDB DOI: https://doi.org/10.2210/pdb4X2A/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-26 Released: 2015-09-16 
• Deposition Author(s): Zhang, H., Zhai, J., Zhang, L., Li, C., Zhao, Y., Hu, X.

---

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 

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

• PubMed: 26268338 
• 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. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 42.34 kDa 
• Atom Count: 2,995 
• Modelled Residue Count: 342 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoylglutathione lyase	A, B	184	Mus musculus	Mutation(s): 0  Gene Names: Glo1 EC: 4.4.1.5
UniProt
Find proteins for Q9CPU0 (Mus musculus) Explore Q9CPU0  Go to UniProtKB:  Q9CPU0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3WL	E [auth A], F [auth B]	5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one C15 H10 O5 FXNFHKRTJBSTCS-UHFFFAOYSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3WL	Binding MOAD:  4X2A	Ki: 183 (nM) from 1 assay(s)
	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 = 41.501	α = 90
b = 64.502	β = 104.79
c = 63.152	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Zhang, H., Zhai, J., Zhang, L., Li, C., Zhao, Y., Hu, X.

Revision History  

• 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