5X79

Human GST Pi conjugated with novel inhibitor, GS-ESF

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

A covalent G-site inhibitor for glutathione S-transferase Pi (GSTP1-1).

Shishido, Y., Tomoike, F., Kimura, Y., Kuwata, K., Yano, T., Fukui, K., Fujikawa, H., Sekido, Y., Murakami-Tonami, Y., Kameda, T., Shuto, S., Abe, H.

(2017) Chem Commun (Camb) 53: 11138-11141

  • DOI: https://doi.org/10.1039/c7cc05829b
  • Primary Citation of Related Structures:  
    5X79

  • PubMed Abstract: 

    We herein report the first covalent G-site-binding inhibitor for GST, GS-ESF (1), which irreversibly inhibited the GSTP 1-1 function. LC-MS/MS and X-ray structure analyses of the covalently linked GST-inhibitor complex suggested that 1 reacted with Tyr108 of GSTP 1-1 . The mechanism of covalent bond formation was discussed based on MD simulation results.

    • Organizational Affiliation: 

    Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-Ku, Nagoya, 464-8602, Japan. h-abe@chem.nagoya-u.ac.jp.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase P
A, B
210Homo sapiensMutation(s): 0 
Gene Names: GSTP1, FAEES3, GST3
EC: 2.5.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P09211 (Homo sapiens)
Explore P09211 
Go to UniProtKB:  P09211
PHAROS:  P09211
GTEx:  ENSG00000084207 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09211
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GF5
Query on GF5
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		(2S)-2-azanyl-5-[[(2R)-3-(2-fluorosulfonylethylsulfanyl)-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-propan-2-yl]amino]-5-oxidanylidene-pentanoic acid
C12 H20 F N3 O8 S2
ICNGQPVIPUWGEA-YUMQZZPRSA-N
MES
Query on MES
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.041α = 90
b = 89.43β = 98.43
c = 68.967γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
MOLREPmodel building
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
JSPS KAKENHI Grant NumberJapan15K12751

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description