3HVH

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

PDB DOI: https://doi.org/10.2210/pdb3HVH/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.153
R-Value Work: 0.130
R-Value Observed: 0.131

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 26.07 kDa
Atom Count: 2,143
Modelled Residue Count: 213
Deposited Residue Count: 221
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22734
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
542 Query on 542 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-[(E)-3-[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-methylaminopurin-9-yl)oxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxy-benzamide C₂₆ H₂₅ F N₆ O₆ NSQDVYXOGVOLPV-WKWRZTKWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CXS Query on CXS Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C₉ H₁₉ N O₃ S PJWWRFATQTVXHA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	I [auth A], J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
542	PDBBind: 3HVH	Ki: 3 (nM) from 1 assay(s)
542	Binding MOAD: 3HVH	Ki: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.153
R-Value Work: 0.130
R-Value Observed: 0.131
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.587	α = 90
b = 56.248	β = 90
c = 78.546	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-10-13

Deposition Author(s):

Revision History (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

3HVH

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)