2C4V

H. pylori type II DHQase in complex with citrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.4 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.


    Related Citations: 
    • Crystal Structure of the Type II 3-Dehydroquinase from Helicobacter Pylori
      Lee, B.I.,Kwak, J.E.,Suh, S.W.
      (2003) Proteins: Struct.,Funct., Genet. 51: 616


    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
167Helicobacter 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CITKd: 2500 nM (100) BINDINGDB
CITKi: 2500000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 
  • Space Group: P 42 3 2
Unit Cell:
Length (Å)Angle (°)
a = 98.910α = 90.00
b = 98.910β = 90.00
c = 98.910γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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
  • Version 1.3: 2019-01-30
    Type: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-02-06
    Type: Data collection, Experimental preparation