2C4W

Type II Dehydroquinase from H. pylori in complex with AH9095

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal Structures of Helicobacter Pylori Type II Dehydroquinase Inhibitor Complexes: New Directions for Inhibitor Design.

Robinson, D.A., Stewart, K.A., Price, N.C., Chalk, P.A., Coggins, J.R., Lapthorn, A.J.

(2006) J.Med.Chem. 49: 1282

  • DOI: 10.1021/jm0505361
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The crystal structures of the type II dehydroquinase (DHQase) from Helicobacter pylori in complex with three competitive inhibitors have been determined. The inhibitors are the substrate analogue 2,3-anhydroquinate (FA1), citrate, and an oxoxanthene ...

    The crystal structures of the type II dehydroquinase (DHQase) from Helicobacter pylori in complex with three competitive inhibitors have been determined. The inhibitors are the substrate analogue 2,3-anhydroquinate (FA1), citrate, and an oxoxanthene sulfonamide derivative (AH9095). Despite the very different chemical nature of the inhibitors, in each case the primary point of interaction with the enzyme is via the residues that bind the C1 functionalities of the substrate, 3-dehydroquinate, i.e., N76, H102, I103, and H104. The DHQase/AH9095 complex crystal structure shows that sulfonamides can form a scaffold for nonsubstrate-like inhibitors and identifies a large conserved hydrophobic patch at the entrance to the active site as a locus that can be exploited in the development of new ligands.

    Organizational Affiliation: 

    Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-DEHYDROQUINATE DEHYDRATASE
A
176Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: aroQ
EC: 4.2.1.10
Find proteins for Q48255 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  Q48255
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GAJ
Query on GAJ
Download SDF File 
Download CCD File 
A
N-TETRAZOL-5-YL 9-OXO-9H-XANTHENE-2 SULPHONAMIDE
N-(1,4-DIHYDRO-5H-TETRAZOL-5-YLIDENE)-9-OXO-9H-XANTHENE-2-SULFONAMIDE
C14 H9 N5 O4 S
HJWYZPGYPZNDTN-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD
Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GAJKi: 20000 nM BINDINGMOAD
GAJKi: 20000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.152 
  • Space Group: F 2 3
Unit Cell:
Length (Å)Angle (°)
a = 131.370α = 90.00
b = 131.370β = 90.00
c = 131.370γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
EPMRphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance