5X79

Human GST Pi conjugated with novel inhibitor, GS-ESF

• PDB DOI: https://doi.org/10.2210/pdb5X79/pdb

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


• Deposited: 2017-02-24 Released: 2017-09-13 
• Deposition Author(s): Tomoike, F., Shishido, Y., Fukui, K., Kimura, Y., Abe, H.
• Funding Organization(s): JSPS KAKENHI Grant Number

---

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 

Starting Model: experimental

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

• PubMed: 28848941 
• 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. [e-mail].

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: 47.98 kDa 
• Atom Count: 4,069 
• Modelled Residue Count: 420 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase P	A, B	210	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GF5	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	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 = 78.041	α = 90
b = 89.43	β = 98.43
c = 68.967	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
MOLREP	model building
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Tomoike, F., Shishido, Y., Fukui, K., Kimura, Y., Abe, H.

---

Funding Organization	Location	Grant Number
JSPS KAKENHI Grant Number	Japan	15K12751

Revision History  

• 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