1KBO

Complex of Human recombinant NAD(P)H:Quinone Oxide reductase type 1 with 5-methoxy-1,2-dimethyl-3-(phenoxymethyl)indole-4,7-dione (ES1340)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of a mechanism-based inhibitor of NAD(P)H:quinone oxidoreductase 1 by biochemical, X-ray crystallographic, and mass spectrometric approaches.

Winski, S.L.Faig, M.Bianchet, M.A.Siegel, D.Swann, E.Fung, K.Duncan, M.W.Moody, C.J.Amzel, L.M.Ross, D.

(2001) Biochemistry 40: 15135-15142

  • Primary Citation of Related Structures:  1KBQ

  • PubMed Abstract: 
  • We report the characterization of 5-methoxy-1,2-dimethyl-3-[(4-nitrophenoxy)methyl]indole-4,7-dione (ES936) as a mechanism-based inhibitor of NQO1. Inactivation of NQO1 by ES936 was time- and concentration-dependent and required the presence of a pyr ...

    We report the characterization of 5-methoxy-1,2-dimethyl-3-[(4-nitrophenoxy)methyl]indole-4,7-dione (ES936) as a mechanism-based inhibitor of NQO1. Inactivation of NQO1 by ES936 was time- and concentration-dependent and required the presence of a pyridine nucleotide cofactor consistent with a need for metabolic activation. That ES936 was an efficient inhibitor was demonstrated in these studies by the low partition ratio (1.40 +/- 0.03). The orientation of ES936 in the active site of NQO1 was examined by X-ray crystallography and found to be opposite to that observed for other indolequinones acting as substrates. ES936 was oriented in such a manner that, after enzymatic reduction and loss of a nitrophenol leaving group, a reactive iminium species was located in close proximity to nucleophilic His 162 and Tyr 127 and Tyr 129 residues in the active site. To determine if ES936 was covalently modifying NQO1, ES936-treated protein was analyzed by electrospray ionization liquid chromatography/mass spectrometry (ESI-LC/MS). The control NQO1 protein had a mass of 30864 +/- 6 Da (n = 20, theoretical, 30868.6 Da) which increased by 217 Da after ES936 treatment (31081 +/- 7 Da, n = 20) in the presence of NADH. The shift in mass was consistent with adduction of NQO1 by the reactive iminium derived from ES936 (M + 218 Da). Chymotryptic digestion of the protein followed by LC/MS analysis located a tetrapeptide spanning amino acids 126-129 which was adducted with the reactive iminium species derived from ES936. LC/MS/MS analysis of the peptide fragment confirmed adduction of either Tyr 127 or Tyr 129 residues. This work demonstrates that ES936 is a potent mechanism-based inhibitor of NQO1 and may be a useful tool in defining the role of NQO1 in cellular systems and in vivo.


    Related Citations: 
    • Structures of Recombinant Mouse and Human NAD(P)H:Quinone Oxidoreductases: Species Comparison and Structural Changes with Substrate Binding and Release
      Faig, M.,Bianchet, M.A.,Chen, S.,Winski, S.L.,Ross, D.,Talalay, P.,Amzel, L.M.
      (2000) Proc.Natl.Acad.Sci.USA 97: 3177
    • Structure-based Development of Anticancer Drugs: Complexes of NAD(P)H:Quinone Reductase 1 with Chemotherapeutic Quinones
      Faig, M.,Bianchet, M.A.,Winski, S.,Hargreaves, R.,Moody, C.J.,Hudnott, A.R.,Ross, D.,Amzel, L.M.
      (2001) Structure 9: 659


    Organizational Affiliation

    Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H dehydrogenase [quinone] 1
A, B, C, D
273Homo sapiensGene Names: NQO1 (DIA4, NMOR1)
EC: 1.6.5.2
Find proteins for P15559 (Homo sapiens)
Go to Gene View: NQO1
Go to UniProtKB:  P15559
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
340
Query on 340

Download SDF File 
Download CCD File 
A, B, C, D
5-METHOXY-1,2-DIMETHYL-3-(PHENOXYMETHYL)INDOLE-4,7-DIONE
C18 H17 N O4
JRPJCFILHCLEJI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.200 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 55.636α = 76.80
b = 57.026β = 76.93
c = 96.878γ = 86.28
Software Package:
Software NamePurpose
CNSrefinement
CCP4model building
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance