Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.67 kDa 
• Atom Count: 1964 
• Modelled Residue Count: 213 
• Deposited Residue Count: 221 
• Unique protein chains: 1

3S68

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

• PDB DOI: 10.2210/pdb3S68/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.217 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

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 D Biol Crystallogr 68: 253-260

• PubMed: 22349227 
• DOI: 10.1107/S0907444912001138
• Primary Citation of Related Structures:  
  3NWB, 3NWE, 3R6T, 3S68, 3U81


• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A	221	Rattus norvegicus	Mutation(s): 0  Gene Names: Comt EC: 2.1.1.6
UniProt
Find proteins for P22734 (Rattus norvegicus) Explore P22734  Go to UniProtKB:  P22734

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	H [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
TCW	G [auth A]	Tolcapone C14 H11 N O5 MIQPIUSUKVNLNT-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TCW	BindingDB:  3S68	IC50: min: 0.91, max: 2200 (nM) from 6 assay(s)
	PDBBind:  3S68	IC50: 2.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.217 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.604	α = 90
b = 50.604	β = 90
c = 168.584	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SADABS	data scaling

Structure Validation

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  

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