3HVI

Rat catechol O-methyltransferase in complex with a catechol-type, N6-ethyladenine-containing bisubstrate inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3HVI/pdb

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


• Deposited: 2009-06-16 Released: 2009-10-13 
• Deposition Author(s): Ehler, A., Schlatter, D., Stihle, M., Benz, J., Rudolph, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.161 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 

Literature

Molecular recognition at the active site of catechol-o-methyltransferase: energetically favorable replacement of a water molecule imported by a bisubstrate inhibitor.

Ellermann, M., Jakob-Roetne, R., Lerner, C., Borroni, E., Schlatter, D., Roth, D., Ehler, A., Rudolph, M.G., Diederich, F.

(2009) Angew Chem Int Ed Engl 48: 9092-9096

• PubMed: 19882607 
• DOI: https://doi.org/10.1002/anie.200904410
• Primary Citation of Related Structures:  
  3HVH, 3HVI, 3HVJ, 3HVK

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Organizational Affiliation: 

Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 25.56 kDa 
• Atom Count: 2,211 
• Modelled Residue Count: 213 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A	221	Rattus norvegicus	Mutation(s): 0  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
619	E [auth A]	N-[(E)-3-[(2R,3S,4R,5R)-5-(6-ethylaminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxy-benzamide C27 H27 F N6 O6 NOCNCHHJBSJZFZ-CJLJSIFTSA-N
D1D	F [auth A]	(4S,5S)-1,2-DITHIANE-4,5-DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-QWWZWVQMSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
619	PDBBind:  3HVI	Ki: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.161 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.857	α = 90
b = 54.706	β = 90
c = 80.617	γ = 90

Software Package:

Software Name	Purpose
COMO	phasing
REFMAC	refinement
XDS	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Ehler, A., Schlatter, D., Stihle, M., Benz, J., Rudolph, M.G.

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-08-08
  Changes: Database references, Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references, Derived calculations