3S68

Rat COMT in complex with SAM and Tolcapone at 1.85A, P3221, Rfree=22.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Catechol-O-methyltransferase in complex with substituted 3'-deoxyribose bisubstrate inhibitors

Ellermann, M.Lerner, C.Burgy, G.Ehler, A.Bissantz, C.Jakob-Roetne, R.Paulini, R.Allemann, O.Tissot, H.Grunstein, D.Stihle, M.Diederich, F.Rudolph, M.G.

(2012) Acta Crystallogr.,Sect.D 68: 253-260

  • DOI: 10.1107/S0907444912001138
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The biological activity of catechol neurotransmitters such as dopamine in the synapse is modulated by transporters and enzymes. Catechol-O-methyltransferase (COMT; EC 2.1.1.6) inactivates neurotransmitters by catalyzing the transfer of a methyl group ...

    The biological activity of catechol neurotransmitters such as dopamine in the synapse is modulated by transporters and enzymes. Catechol-O-methyltransferase (COMT; EC 2.1.1.6) inactivates neurotransmitters by catalyzing the transfer of a methyl group from S-adenosylmethionine to catechols in the presence of Mg²⁺. This pathway also inactivates L-DOPA, the standard therapeutic for Parkinson's disease. Depletion of catechol neurotransmitters in the prefrontal cortex has been linked to schizophrenia. The inhibition of COMT therefore promises improvements in the treatment of these diseases. The concept of bisubstrate inhibitors for COMT has been described previously. Here, ribose-modified bisubstrate inhibitors were studied. Three high-resolution crystal structures of COMT in complex with novel ribose-modified bisubstrate inhibitors confirmed the predicted binding mode but displayed subtle alterations at the ribose-binding site. The high affinity of the inhibitors can be convincingly rationalized from the structures, which document the possibility of removing and/or replacing the ribose 3'-hydroxyl group and provide a framework for further inhibitor design.


    Organizational Affiliation

    Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, CH-8093 Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catechol O-methyltransferase
A
221Rattus norvegicusMutation(s): 0 
Gene 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
TCW
Query on TCW

Download SDF File 
Download CCD File 
A
Tolcapone
(3,4-dihydroxy-5-nitrophenyl)(4-methylphenyl)methanone
C14 H11 N O5
MIQPIUSUKVNLNT-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 %)
TCWIC50: 2.2 - 2200 nM (100) BINDINGDB
TCWIC50: 2.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.168 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 50.604α = 90.00
b = 50.604β = 90.00
c = 168.584γ = 120.00
Software Package:
Software NamePurpose
SADABSdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-02-22
    Type: Database references
  • Version 1.2: 2012-04-11
    Type: Database references
  • Version 1.3: 2012-05-23
    Type: Structure summary
  • Version 1.4: 2017-11-08
    Type: Refinement description