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


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 

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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-DEHYDROQUINATE DEHYDRATASE
A, B, C
167Helicobacter pyloriMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ48255
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XD9
Query on XD9

Download Ideal Coordinates CCD File 
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
Binding Affinity Annotations 
IDSourceBinding Affinity
XD9 Binding MOAD:  2XD9 Ki: 350 (nM) from 1 assay(s)
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 = 100.217α = 90
b = 100.217β = 90
c = 103.934γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

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