3VW9 | pdb_00003vw9

Human Glyoxalase I with an N-hydroxypyridone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3VW9/pdb

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


• Deposited: 2012-08-10 Released: 2012-12-12 
• Deposition Author(s): Fukami, T.A., Irie, M., Matsuura, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.193 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 23122816 
• DOI: https://doi.org/10.1016/j.bmcl.2012.10.045
• Primary Citation Related Structures: 
  3VW9


• 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.

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

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: 43.29 kDa 
• Atom Count: 3,404 
• Modeled Residue Count: 352 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoylglutathione lyase	A, B	187	Homo sapiens	Mutation(s): 0  Gene Names: GLO1 EC: 4.4.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q04760 (Homo sapiens) Explore Q04760  Go to UniProtKB:  Q04760
PHAROS:  Q04760 GTEx:  ENSG00000124767

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HPJ	E [auth A], G [auth B]	1-hydroxy-6-[1-(3-methoxypropyl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-4-phenylpyridin-2(1H)-one C22 H21 N3 O3 MIWLVFZOCHMICD-UHFFFAOYSA-N
EPE	D [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HPJ	BindingDB:  3VW9	Ki: 11 (nM) from 1 assay(s)
		IC50: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.193 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.99	α = 90
b = 66.98	β = 90
c = 68.53	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-12 
Deposition Author(s): Fukami, T.A., Irie, M., Matsuura, T.

Revision History  

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