2XD9

STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-4,6,7-Trihydroxy-2-((E)-prop-1- enyl)-4,5,6,7-tetrahydrobenzo(b)thiophene-4-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb2XD9/pdb

Classification: LYASE
Organism(s): Helicobacter pylori
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-04-30 Released: 2010-11-24
Deposition Author(s): Paz, S., Tizon, L., Otero, J.M., Llamas-Saiz, A.L., Fox, G.C., van Raaij, M.J., Lamb, H., Hawkins, A.R., Lapthorn, A.J., Castedo, L., Gonzalez-Bello, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.250
R-Value Work: 0.210
R-Value Observed: 0.212

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Tetrahydrobenzothiophene derivatives: conformationally restricted inhibitors of type II dehydroquinase.

Paz, S., Tizon, L., Otero, J.M., Llamas-Saiz, A.L., Fox, G.C., van Raaij, M.J., Lamb, H., Hawkins, A.R., Lapthorn, A.J., Castedo, L., Gonzalez-Bello, C.

(2011) ChemMedChem 6: 266-272

PubMed: 21275050 Search on PubMed
DOI: https://doi.org/10.1002/cmdc.201000343
Primary Citation of Related Structures:
2XD9, 2XDA

Organizational Affiliation

Departamento de Química Orgánica y Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Universidad de Santiago de Compostela calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.

Macromolecule Content

Total Structure Weight: 56.31 kDa
Atom Count: 3,944
Modelled Residue Count: 457
Deposited Residue Count: 501
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B, C	167	Helicobacter pylori	Mutation(s): 0 EC: 4.2.1.10
UniProt
Find proteins for Q48255 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore Q48255 Go to UniProtKB: Q48255
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q48255
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XD9 Query on XD9 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	(4R,6R,7S)-4,6,7-TRIHYDROXY-2-[(1E)-PROP-1-EN-1-YL]-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-4-CARBOXYLIC ACID C₁₂ H₁₄ O₅ S XBFFFFBWIVSOII-PJMUFDJCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
XD9	PDBBind: 2XD9	Ki: 350 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.250
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.217	α = 90
b = 100.217	β = 90
c = 103.934	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-11-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-11-24
Type: Initial release
Version 1.1: 2011-12-21
Changes: Database references, Version format compliance
Version 1.2: 2012-10-31
Changes: Database references
Version 1.3: 2018-02-07
Changes: Database references, Structure summary
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description