3W0T

Human Glyoxalase I with an N-hydroxypyridone derivative inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

N-Hydroxypyridone-based glyoxalase I inhibitors mimicking binding interactions of the substrate

Koyano, H.Aoki, T.Yamamoto, S.Kobayashi, T.Miura, T.Ohara, K.Fukami, T.A.Irie, M.Sakamoto, H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lactoylglutathione lyase
A, B, C, D
187Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04760
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HPU
Query on HPU

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
L [auth C],
O [auth D]
N-[3-(1-hydroxy-6-oxo-4-phenyl-1,6-dihydropyridin-2-yl)phenyl]methanesulfonamide
C18 H16 N2 O4 S
MDYXMYBWSBAIMZ-UHFFFAOYSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B],
N [auth D]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
K [auth C],
M [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.57α = 90
b = 81.03β = 90.13
c = 68.62γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description