4KYH | pdb_00004kyh

Crystal structure of mouse glyoxalase I complexed with zopolrestat

PDB DOI: https://doi.org/10.2210/pdb4KYH/pdb

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

Deposited: 2013-05-29 Released: 2013-08-07
Deposition Author(s): Zhai, J., Yuan, M., Zhang, L., Chen, Y., Zhang, H., Chen, S., Zhao, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.236 (Depositor), 0.234 (DCC)
R-Value Work:
0.172 (Depositor), 0.170 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4KYH

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Zopolrestat as a human glyoxalase I inhibitor and its structural basis.

Zhai, J., Zhang, H., Zhang, L., Zhao, Y., Chen, S., Chen, Y., Peng, X., Li, Q., Yuan, M., Hu, X.

(2013) ChemMedChem 8: 1462-1464

PubMed: 23857942 Search on PubMed
DOI: https://doi.org/10.1002/cmdc.201300243
Primary Citation Related Structures:
4KYH, 4KYK

Organizational Affiliation

Centre for Cellular & Structural Biology, School of Pharmaceutical Sciences, Sun Yat-sen University, 132 East Circle, University City, Guangzhou 510006, P.R. China.

Macromolecule Content

Total Structure Weight: 42.22 kDa
Atom Count: 2,955
Modeled Residue Count: 353
Deposited Residue Count: 368
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CPU0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZST Query on ZST Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	3,4-DIHYDRO-4-OXO-3-((5-TRIFLUOROMETHYL-2-BENZOTHIAZOLYL)METHYL)-1-PHTHALAZINE ACETIC ACID C₁₉ H₁₂ F₃ N₃ O₃ S BCSVCWVQNOXFGL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
ZST	BindingDB: 4KYH	Ki: 1.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.236 (Depositor), 0.234 (DCC)
R-Value Work: 0.172 (Depositor), 0.170 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.781	α = 90
b = 64.716	β = 101.9
c = 65.361	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
REFMAC	refinement
CrysalisPro	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-08-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-07
Type: Initial release
Version 1.1: 2019-12-04
Changes: Data collection
Version 1.2: 2022-08-24
Changes: Database references, Derived calculations
Version 1.3: 2024-05-29
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.