3NVY

Crystal Structure of Bovine Xanthine Oxidase in Complex with Quercetin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray Crystal Structure of a Xanthine Oxidase Complex with the Flavonoid Inhibitor Quercetin.

Cao, H.Pauff, J.M.Hille, R.

(2014) J Nat Prod 77: 1693-1699

  • DOI: 10.1021/np500320g

  • PubMed Abstract: 
  • Xanthine oxidase catalyzes the sequential hydroxylation of hypoxanthine to uric acid via xanthine as intermediate. Deposition of crystals of the catalytic product uric acid or its monosodium salt in human joints with accompanying joint inflammation i ...

    Xanthine oxidase catalyzes the sequential hydroxylation of hypoxanthine to uric acid via xanthine as intermediate. Deposition of crystals of the catalytic product uric acid or its monosodium salt in human joints with accompanying joint inflammation is the major cause of gout. Natural flavonoids are attractive leads for rational design of preventive and therapeutic xanthine oxidase inhibitors due to their beneficial antioxidant, anti-inflammatory, and antiproliferative activities in addition to their micromolar inhibitory activities toward xanthine oxidase. We determined the first complex X-ray structure of mammalian xanthine oxidase with the natural flavonoid inhibitor quercetin at 2.0 Å resolution. The inhibitor adopts a single orientation with its benzopyran moiety sandwiched between Phe 914 and Phe 1009 and ring B pointing toward the solvent channel leading to the molybdenum active center. The favorable steric complementarity of the conjugated three-ring structure of quercetin with the active site and specific hydrogen-bonding interactions of exocyclic hydroxy groups with catalytically relevant residues Arg 880 and Glu 802 correlate well with a previously reported structure-activity relationship of flavonoid inhibitors of xanthine oxidase. The current complex provides a structural basis for the rational design of flavonoid-type inhibitors against xanthine oxidase useful for the treatment of hyperuricemia, gout, and inflammatory disease states.


    Organizational Affiliation

    Department of Biochemistry, University of California , Riverside, California 92521, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xanthine dehydrogenase/oxidase
A, J
164Bos taurusMutation(s): 0 
Gene Names: XDH
Find proteins for P80457 (Bos taurus)
Go to Gene View: XDH
Go to UniProtKB:  P80457
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Xanthine dehydrogenase/oxidase
B, K
334Bos taurusMutation(s): 0 
Gene Names: XDH
Find proteins for P80457 (Bos taurus)
Go to Gene View: XDH
Go to UniProtKB:  P80457
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Xanthine dehydrogenase/oxidase
C, L
756Bos taurusMutation(s): 0 
Gene Names: XDH
Find proteins for P80457 (Bos taurus)
Go to Gene View: XDH
Go to UniProtKB:  P80457
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QUE
Query on QUE

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Download CCD File 
C, L
3,5,7,3',4'-PENTAHYDROXYFLAVONE
QUERCETIN
C15 H10 O7
REFJWTPEDVJJIY-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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

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Download CCD File 
C, L
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C10 H14 N5 O6 P S2
HPEUEJRPDGMIMY-IFQPEPLCSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
A, J
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MOS
Query on MOS

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Download CCD File 
C, L
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QUEKi: 1200 nM (100) BINDINGDB
QUEIC50: 2620 - 3500 nM (88) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 132.686α = 90.00
b = 73.398β = 97.13
c = 138.210γ = 90.00
Software Package:
Software NamePurpose
CCP4phasing
PDB_EXTRACTdata extraction
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-07-08 
  • Released Date: 2011-01-19 
  • Deposition Author(s): Cao, H., Hille, R.

Revision History 

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-09-03
    Type: Database references