3S68

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

Structural Biology Knowledgebase: 3S68 SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3S68

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 25670.90

Macromolecule Entities
Molecule Chains Length Organism Details
Catechol O-methyltransferase A 221 Rattus norvegicus EC#: 2.1.1.6 IUBMB
Fragment: SOLUBLE FORM, RESIDUES 44-264
Gene Name(s): Comt

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SAM
Query on SAM

A S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TCW
Query on TCW

A Tolcapone
(3,4-dihydroxy-5-nitrophenyl)(4-methylphenyl)methanone (Synonym)
C14 H11 N O5
MIQPIUSUKVNLNT-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TCW IC50: 2.2 - 2200 nM (100) BindingDB

N/A in BindingMoad
IC50: 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
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 50.60 α = 90.00
b = 50.60 β = 90.00
c = 168.58 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-25
  • Released Date: 2012-02-01
  • Deposition author(s): Ehler, A., Schlatter, D., Stihle, M., Benz, J., Rudolph, M.G.

Revision History

  • 2012-05-23
    Type: Entry authorship | Details: --
  • 2012-04-11
    Type: Citation | Details: Citation update
  • 2012-02-22
    Type: Citation | Details: Citation update