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


This is version 1.3 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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-DEHYDROQUINATE DEHYDRATASE
A, B, C
167Helicobacter pyloriMutation(s): 0 
EC: 4.2.1.10
Find proteins for Q48255 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  Q48255
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XD9
Query on XD9

Download CCD File 
A, B, 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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XD9Ki:  350   nM  Binding MOAD
XD9Ki:  350   nM  PDBBind
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



Entry History 

Deposition Data

Revision History 

  • 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