2ZVJ

Crystal structures of rat Catechol-O-Methyltransferase complexed with coumarine-based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.219 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of rat catechol-O-methyltransferase complexed with coumarine-based inhibitor

Tsuji, E.Okazaki, K.Takeda, K.

(2009) Biochem Biophys Res Commun 378: 494-497

  • DOI: https://doi.org/10.1016/j.bbrc.2008.11.085
  • Primary Citation of Related Structures:  
    2ZVJ

  • PubMed Abstract: 

    In human, catechol-O-methyltransferase (COMT: E.C. 2.1.1.6) is responsible for metabolism of catechol neurotransmitter and xenobiotics. The main clinical interest in COMT results from the possibility of using COMT inhibitors as adjuncts in the therapy of Parkinson's disease (PD) with l-DOPA. COMT is therefore a target for inhibitor development aiming at PD treatment and has been submitted to extensive structure-based drug design. Recently reported inhibitors have nitrocatechol structure that may inhibit oxidative phosphorylation and uncouple mitochondrial energy production. This work reports the first crystallographic study of Rat COMT complexed with non-nitrocatechol inhibitor. Analysis of the structural differences among the previously reported inhibitor complexes, coumarine-based inhibitor (4-phenyl-7, 8-dihydroxycoumarine: 4PCM) bound structure provides the explanation for inhibitor binding and can be used for future inhibitor design.


  • Organizational Affiliation

    Molecular Design Research, R&D Kissei Pharmaceutical Co., Ltd. 4365-1 Kashiwabara, Hotaka, Azumino-city, Nagano 399-8304, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catechol O-methyltransferase223Rattus norvegicusMutation(s): 0 
EC: 2.1.1.6
UniProt
Find proteins for P22734 (Rattus norvegicus)
Explore P22734 
Go to UniProtKB:  P22734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22734
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
C [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
KOM
Query on KOM

Download Ideal Coordinates CCD File 
D [auth A]7,8-dihydroxy-4-phenyl-2H-chromen-2-one
C15 H10 O4
JRVIIPJSVKTPBK-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KOM PDBBind:  2ZVJ IC50: 1800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.219 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.448α = 90
b = 50.448β = 90
c = 167.626γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
BBSdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2009-01-06 
  • Deposition Author(s): Tsuji, E.

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description