3GUR

Crystal Structure of mu class glutathione S-transferase (GSTM2-2) in complex with glutathione and 6-(7-Nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol (NBDHEX)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


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

Literature

Structural basis for the binding of the anticancer compound 6-(7-nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol to human glutathione s-transferases

Federici, L., Lo Sterzo, C., Pezzola, S., Di Matteo, A., Scaloni, F., Federici, G., Caccuri, A.M.

(2009) Cancer Res. 69: 8025-8034

  • DOI: 10.1158/0008-5472.CAN-09-1314
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Glutathione S-transferases (GST) constitute a superfamily of enzymes with diversified functions including detoxification from xenobiotics. In many human cancers, Pi class GST (GSTP1-1) is overexpressed and contributes to multidrug resistance by conju ...

    Glutathione S-transferases (GST) constitute a superfamily of enzymes with diversified functions including detoxification from xenobiotics. In many human cancers, Pi class GST (GSTP1-1) is overexpressed and contributes to multidrug resistance by conjugating chemotherapeutics. In addition, GSTP1-1 displays antiapoptotic activity by interacting with c-Jun NH(2)-terminal kinase, a key regulator of apoptosis. Therefore, GSTP1-1 is considered a promising target for pharmaceutical treatment. Recently, a potent inhibitor of GSTs, 6-(7-nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol (NBDHEX), was identified and tested on several tumor cell lines demonstrating high antiproliferative activity. To establish the structural basis of NBDHEX activity, we determined the crystal structure of NBDHEX bound to either GSTP1-1 or GSTM2-2 (mu class). NBDHEX in both cases binds to the H-site but occupies different positions. Furthermore, the compound is covalently attached to the GSH sulfur in the GSTM2-2 crystal, forming a sigma-complex, although it is bound but not conjugated in the GSTP1-1 crystal. Several differences in the H-sites of the two isozymes determine the higher affinity of NBDHEX for GSTM2-2 with respect to GSTP1-1. One such difference is the presence of Ile(104) in GSTP1-1 close to the bound NBDHEX, whereas the corresponding position is occupied by an alanine in GSTM2-2. Mutation of Ile(104) into valine is a frequent GSTP1-1 polymorphism and we show here that the Ile(104)Val and Ile(104)Ala variants display a 4-fold higher affinity for the compound. Remarkably, the GSTP1-1/Ile(104)Ala structure in complex with NBDHEX shows a considerable shift of the compound inside the H-site. These data might be useful for the development of new anticancer compounds.

    Organizational Affiliation: 

    Department of Biomedical Sciences, University of Chieti, CeSI Center of Excellence on Aging, G D'Annunzio University Foundation, Chieti, Italy. lfederici@unich.it.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutathione S-transferase Mu 2
A, B, C, D
217Homo sapiensMutation(s): 0 
Gene Names: GSTM2 (GST4)
EC: 2.5.1.18
Find proteins for P28161 (Homo sapiens)
Go to Gene View: GSTM2
Go to UniProtKB:  P28161
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSH
Query on GSH
Download SDF File 
Download CCD File 
B, D
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
BYG
Query on BYG
Download SDF File 
Download CCD File 
A, C
L-gamma-glutamyl-S-{(4R)-4-[(6-hydroxyhexyl)sulfanyl]-7-nitro-4,5-dihydro-2,1,3-benzoxadiazol-4-yl}-L-cysteinylglycine
C22 H32 N6 O10 S2
DZIARIAPFJPVSN-FBJOKTGGSA-N
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BYGIC50: 10 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.750α = 90.00
b = 78.016β = 90.00
c = 219.362γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
MOLREPphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-12-14
    Type: Non-polymer description, Structure summary
  • Version 1.3: 2017-11-01
    Type: Refinement description