1QBG

CRYSTAL STRUCTURE OF HUMAN DT-DIAPHORASE (NAD(P)H OXIDOREDUCTASE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human DT-diaphorase: a model for interaction with the cytotoxic prodrug 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB1954).

Skelly, J.V.Sanderson, M.R.Suter, D.A.Baumann, U.Read, M.A.Gregory, D.S.Bennett, M.Hobbs, S.M.Neidle, S.

(1999) J.Med.Chem. 42: 4325-4330


  • PubMed Abstract: 
  • The crystal structure of human DT-diaphorase (NAD(P)H oxidoreductase (quinone); EC 1.6.99.2) has been determined to 2.3 A resolution. There are only minor differences in shape and volume between the active sites of the rat and human enzymes and in th ...

    The crystal structure of human DT-diaphorase (NAD(P)H oxidoreductase (quinone); EC 1.6.99.2) has been determined to 2.3 A resolution. There are only minor differences in shape and volume between the active sites of the rat and human enzymes and in the hydrophobic environment in the vicinity of the substrate. The isoalloxazine ring of the bound FAD is more buried in the human structure. Molecular modeling was used to examine optimal positions for the antitumor prodrug CB1954 (5-(aziridin-1-yl)-2,4-dinitrobenzamide) in both the human and rat enzyme active sites. This suggests that the position of CB1954 in the active site of the human enzyme is very similar to that in the rat, although there are detailed differences in the predicted patterns of hydrogen bonding between side chains and the drug. Some of the differences are a consequence of the shift in position for the FAD molecule and may contribute to the observed differences in rate of the two-electron reduction of CB1954.


    Organizational Affiliation

    CRC Biomolecular Structure Unit and CRC Centre for Cancer Therapeutics, The Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H DEHYDROGENASE [QUINONE] 1
A, B, C, D
272Homo sapiensMutation(s): 0 
Gene 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 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 55.880α = 77.10
b = 57.490β = 76.20
c = 98.770γ = 86.90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description