2CL5

Catechol-O-methyltransferase in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comparative Study of Ortho- and Meta-Nitrated Inhibitors of Catechol-O-Methyltransferase: Interactions with the Active Site and Regioselectivity of O-Methylation.

Palma, P.N.Rodrigues, M.L.Archer, M.Bonifacio, M.J.Loureiro, A.I.Learmonth, D.A.Carrondo, M.A.Soares-Da-Silva, P.

(2006) Mol.Pharmacol. 70: 143

  • DOI: 10.1124/mol.106.023119

  • PubMed Abstract: 
  • In this work, we present a comparative case study of "ortho-" and "meta-nitrated" catecholic inhibitors of catechol-O-methyltransferase (COMT), with regard to their interaction with the catalytic site of the enzyme and the in vitro regioselective for ...

    In this work, we present a comparative case study of "ortho-" and "meta-nitrated" catecholic inhibitors of catechol-O-methyltransferase (COMT), with regard to their interaction with the catalytic site of the enzyme and the in vitro regioselective formation of their mono-O-methyl ether metabolites. In particular, the effects of altering the attachment position of the inhibitors' side-chain substituent, within the classic nitrocatechol pharmacophore, were investigated. For this purpose, we compared two simple regioisomeric nitrocatechol-type inhibitors of COMT, BIA 3-228 and BIA 8-176, which contain the benzoyl substituent attached at the meta and ortho positions, respectively, relative to the nitro group. The two compounds were slowly O-methylated by COMT in vitro, but the particular substitution pattern of each compound was shown to have a profound impact on the regioselectivity of their O-methylation. To provide a plausible interpretation of these results, a comprehensive analysis of the protein-inhibitor interactions and of the relative chemical susceptibility to O-methylation of the catechol hydroxyl groups was performed by means of docking simulations and ab initio molecular orbital calculations. The major structural and chemical factors that determine the enzyme regioselectivity of O-methylation were identified, and the X-ray structure of the complex of COMT with S-adenosyl-l-methionine and BIA 8-176 is herein disclosed. This is the first reported structure of the soluble form of COMT complexed with a nitrocatecholic inhibitor having a bulky substituent group in adjacent position (ortho) to the nitro group. Structural and dynamic aspects of this complex are analyzed and discussed, in the context of the present study.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Studies of a Catechol-O-Methyltransferase-Inhibitor Complex
      Rodrigues, M.L.,Bonifacio, M.J.,Soares-Da-Silva, P.,Carrondo, M.A.,Archer, M.
      (2005) Acta Crystallogr.,Sect.D 61: 118


    Organizational Affiliation

    Department of Research and Development, Bial., A. Av. da Siderurgia Nacional, 4745-457 S. Mamede do Coronado, Trofa, Portugal. nuno.palma@bial.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATECHOL O-METHYLTRANSFERASE
A, B
221Rattus norvegicusGene Names: Comt
EC: 2.1.1.6
Find proteins for P22734 (Rattus norvegicus)
Go to UniProtKB:  P22734
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU3
Query on BU3

Download SDF File 
Download CCD File 
A, B
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
 Ligand Interaction
BIE
Query on BIE

Download SDF File 
Download CCD File 
A, B
(3,4-DIHYDROXY-2-NITROPHENYL)(PHENYL)METHANONE
BIA 3-335
C13 H9 N O5
ICLKAUQIPVFHOI-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

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Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.149 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.767α = 90.00
b = 79.627β = 91.14
c = 61.540γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance