3HVI | pdb_00003hvi

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.161 (Depositor), 0.159 (DCC)
R-Value Work:
0.131 (Depositor), 0.129 (DCC)
R-Value Observed:
0.132 (Depositor)

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 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: 25.56 kDa
Atom Count: 2,211
Modeled Residue Count: 213
Deposited Residue Count: 221
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22734
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
619 Query on 619 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
D1D Query on D1D Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(4S,5S)-1,2-DITHIANE-4,5-DIOL C₄ H₈ O₂ S₂ YPGMOWHXEQDBBV-QWWZWVQMSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.161 (Depositor), 0.159 (DCC)
R-Value Work: 0.131 (Depositor), 0.129 (DCC)
R-Value Observed: 0.132 (Depositor)

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

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Ligand Structure Quality Assessment

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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