7WT0 | pdb_00007wt0

human glyoxalase I (with C-ter His tag) in complex with TLSC702

• PDB DOI: https://doi.org/10.2210/pdb7WT0/pdb

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


• Deposited: 2022-02-03 Released: 2022-04-13 
• Deposition Author(s): Usami, M., Yokoyama, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of human glyoxalase I and its complex with TLSC702 reveal inhibitor binding mode and substrate preference.

Usami, M., Ando, K., Shibuya, A., Takasawa, R., Yokoyama, H.

(2022) FEBS Lett 596: 1458-1467

• PubMed: 35363883 
• DOI: https://doi.org/10.1002/1873-3468.14344
• Primary Citation of Related Structures:  
  7WSZ, 7WT0, 7WT1, 7WT2


• PubMed Abstract: 
  

  Human glyoxalase I (hGLO I) is an enzyme for detoxification of methylglyoxal (MG) and has been considered an attractive target for the development of new anticancer drugs. In our previous report, the GLO I inhibitor TLSC702 induced apoptosis in tumor cells. Here, we determined the crystal structures of hGLO I and its complex with TLSC702. In the complex, the carboxyl O atom of TLSC702 is coordinated to Zn ²⁺ , and TLSC702 mainly shows van der Waals interaction with hydrophobic residues. In the inhibitor-unbound structure, glycerol, which has similar functional groups to MG, was bound to Zn ²⁺ , indicating that GLO I can easily bind to MG. This study provides a structural basis to develop better anticancer drugs.

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Organizational Affiliation: 

Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, 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: 44.53 kDa 
• Atom Count: 3,069 
• Modelled Residue Count: 368 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoylglutathione lyase	A, B	192	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5ZO (Subject of Investigation/LOI)	D [auth A], F [auth B]	(~{E})-3-(1,3-benzothiazol-2-yl)-4-(4-methoxyphenyl)but-3-enoic acid C18 H15 N O3 S SONSOTYJHQIJQV-JLHYYAGUSA-N
ZN (Subject of Investigation/LOI)	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5ZO	BindingDB:  7WT0	IC50: 2300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.689	α = 90
b = 81.971	β = 93.85
c = 46.927	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-13 
Deposition Author(s): Usami, M., Yokoyama, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	17K07316

Revision History  

• Version 1.0: 2022-04-13
  Type: Initial release
  
• Version 1.1: 2022-06-29
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description