1SG0

Crystal structure analysis of QR2 in complex with resveratrol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of quinone reductase 2 in complex with resveratrol

Buryanovskyy, L.Fu, Y.Boyd, M.Ma, Y.Hsieh, T.C.Wu, J.M.Zhang, Z.

(2004) Biochemistry 43: 11417-11426

  • DOI: 10.1021/bi049162o
  • Primary Citation of Related Structures:  
    1SG0

  • PubMed Abstract: 
  • Resveratrol has been shown to have chemopreventive, cardioprotective, and antiaging properties. Here, we report that resveratrol is a potent inhibitor of quinone reductase 2 (QR2) activity in vitro with a dissociation constant of 35 nM and show that ...

    Resveratrol has been shown to have chemopreventive, cardioprotective, and antiaging properties. Here, we report that resveratrol is a potent inhibitor of quinone reductase 2 (QR2) activity in vitro with a dissociation constant of 35 nM and show that it specifically binds to the deep active-site cleft of QR2 using high-resolution structural analysis. All three resveratrol hydroxyl groups form hydrogen bonds with amino acids from QR2, anchoring a flat resveratrol molecule in parallel with the isoalloxazine ring of FAD. The unique active-site pocket in QR2 could potentially bind other natural polyphenols such as flavonoids, as proven by the high affinity exhibited by quercetin toward QR2. K562 cells with QR2 expression suppressed by RNAi showed similar properties as resveratrol-treated cells in their resistance to quinone toxicity. Furthermore, the QR2 knockdown K562 cells exhibit increased antioxidant and detoxification enzyme expression and reduced proliferation rates. These observations could imply that the chemopreventive and cardioprotective properties of resveratrol are possibly the results of QR2 activity inhibition, which in turn, up-regulates the expression of cellular antioxidant enzymes and cellular resistance to oxidative stress.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NRH dehydrogenase [quinone] 2AB230Homo sapiensMutation(s): 0 
Gene Names: NQO2NMOR2BC006096
EC: 1.6.99.2 (PDB Primary Data), 1.10.5.1 (UniProt)
Find proteins for P16083 (Homo sapiens)
Explore P16083 
Go to UniProtKB:  P16083
NIH Common Fund Data Resources
PHAROS  P16083
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

Download CCD File 
A, B
RESVERATROL
C14 H12 O3
LUKBXSAWLPMMSZ-OWOJBTEDSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
STLIC50:  450   nM  BindingDB
STLIC50:  913   nM  BindingDB
STLIC50:  6900   nM  BindingDB
STLKi:  88   nM  BindingDB
STLKd:  35   nM  Binding MOAD
STLKd:  54   nM  BindingDB
STLIC50:  1400   nM  BindingDB
STLΔG:  40.959999084472656   kJ/mol  BindingDB
STLIC50:  960   nM  BindingDB
STL-TΔS:  20.93000030517578   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.33α = 90
b = 106.372β = 90
c = 56.982γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance