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 
  • R-Value Observed: 0.156 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1021/jm0505361
  • Primary Citation of Related Structures:  
    2C4V, 2C4W, 2C57

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-DEHYDROQUINATE DEHYDRATASE176Helicobacter 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.156 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.37α = 90
b = 131.37β = 90
c = 131.37γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description