2ZVJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.bbrc.2008.11.085

  • 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 therap ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catechol O-methyltransferase
A
223Rattus norvegicusGene Names: Comt
EC: 2.1.1.6
Find proteins for P22734 (Rattus norvegicus)
Go to UniProtKB:  P22734
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KOM
Query on KOM

Download SDF File 
Download CCD File 
A
7,8-dihydroxy-4-phenyl-2H-chromen-2-one
4-phenyl-7,8-dihydroxycoumarine
C15 H10 O4
JRVIIPJSVKTPBK-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KOMIC50: 1800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.211 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 50.448α = 90.00
b = 50.448β = 90.00
c = 167.626γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
BBSdata collection
REFMACrefinement
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-11-07 
  • Released Date: 2009-01-06 
  • Deposition Author(s): Tsuji, E.

Revision History 

  • Version 1.0: 2009-01-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance