3FW1

Quinone Reductase 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The structure of the leukemia drug imatinib bound to human quinone reductase 2 (NQO2).

Winger, J.A.Hantschel, O.Superti-Furga, G.Kuriyan, J.

(2009) BMC Struct Biol 9: 7-7

  • DOI: 10.1186/1472-6807-9-7
  • Primary Citation of Related Structures:  
    3FW1

  • PubMed Abstract: 
  • Imatinib represents the first in a class of drugs targeted against chronic myelogenous leukemia to enter the clinic, showing excellent efficacy and specificity for Abl, Kit, and PDGFR kinases. Recent screens carried out to find off-target proteins that bind to imatinib identified the oxidoreductase NQO2, a flavoprotein that is phosphorylated in a chronic myelogenous leukemia cell line ...

    Imatinib represents the first in a class of drugs targeted against chronic myelogenous leukemia to enter the clinic, showing excellent efficacy and specificity for Abl, Kit, and PDGFR kinases. Recent screens carried out to find off-target proteins that bind to imatinib identified the oxidoreductase NQO2, a flavoprotein that is phosphorylated in a chronic myelogenous leukemia cell line.


    Organizational Affiliation

    Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, Howard Hughes Medical Institute, University of California, Berkeley, USA. wingerj@berkeley.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosyldihydronicotinamide dehydrogenase [quinone]A233Homo sapiensMutation(s): 0 
Gene Names: NMOR2NQO2
EC: 1.10.99.2 (PDB Primary Data), 1.10.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P16083 (Homo sapiens)
Explore P16083 
Go to UniProtKB:  P16083
PHAROS:  P16083
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
STI (Subject of Investigation/LOI)
Query on STI

Download Ideal Coordinates CCD File 
D [auth A]4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE
C29 H31 N7 O
KTUFNOKKBVMGRW-UHFFFAOYSA-N
 Ligand Interaction
MRD
Query on MRD

Download Ideal Coordinates CCD File 
E [auth A], F [auth A](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
STI BindingDB:  3FW1 Ki: 39 (nM) from 1 assay(s)
IC50: min: 43, max: 400 (nM) from 3 assay(s)
Binding MOAD:  3FW1 IC50: 80 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.337α = 90
b = 100.337β = 90
c = 104.858γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance