2WKS

Structure of Helicobacter pylori Type II Dehydroquinase with a new carbasugar-thiophene inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Synthesis and biological evaluation of new nanomolar competitive inhibitors of Helicobacter pylori type II dehydroquinase. Structural details of the role of the aromatic moieties with essential residues.

Prazeres, V.F.Tizon, L.Otero, J.M.Guardado-Calvo, P.Llamas-Saiz, A.L.van Raaij, M.J.Castedo, L.Lamb, H.Hawkins, A.R.Gonzalez-Bello, C.

(2010) J Med Chem 53: 191-200

  • DOI: 10.1021/jm9010466
  • Primary Citation of Related Structures:  
    2WKS

  • PubMed Abstract: 
  • The shikimic acid pathway is essential to many pathogens but absent in mammals. Enzymes in its pathway are therefore appropriate targets for the development of novel antibiotics. Dehydroquinase is the third enzyme of the pathway, catalyzing the reversible dehydratation of 3-dehydroquinic acid to form 3-dehydroshikimic acid ...

    The shikimic acid pathway is essential to many pathogens but absent in mammals. Enzymes in its pathway are therefore appropriate targets for the development of novel antibiotics. Dehydroquinase is the third enzyme of the pathway, catalyzing the reversible dehydratation of 3-dehydroquinic acid to form 3-dehydroshikimic acid. Here we present the synthesis of novel inhibitors with high affinity for Helicobacter pylori type II dehydroquinase and efficient inhibition characteristics. The structure of Helicobacter pylori type II dehydroquinase in complex with the most potent inhibitor shows that the aromatic functional group interacts with the catalytic Tyr22 by pi-stacking, expelling the Arg17 side chain, which is essential for catalysis, from the active site. The structure therefore explains the favorable properties of the inhibitor and will aid in design of improved antibiotics.


    Related Citations: 
    • Progress in Type II Dehydroquinase Inhibitors: From Concept to Practice.
      Gonzalez-Bello, C., Castedo, L.
      (2007) Med Res Rev 27: 177
    • Competitive Inhibitors of Helicobacter Pylori Type II Dehydroquinase: Synthesis, Biological Evaluation, and NMR Studies.
      Prazeres, V.F.V., Sanchez-Sixto, C., Castedo, L., Shuh, S.W., Lamb, H., Hawkins, A.R., Canada, F.J., Jimenez-Barbero, J., Gonzalez-Bello, C.
      (2008) ChemMedChem 3: 756

    Organizational Affiliation

    Laboratorio de Quimica Organica (CSIC) y Departamento de Quimica Organica, Facultad de Quimica, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-DEHYDROQUINATE DEHYDRATASEA, B, C, D, E, F167Helicobacter 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CB6 (Subject of Investigation/LOI)
Query on CB6

Download Ideal Coordinates CCD File 
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F](1R,4S,5R)-1,4,5-trihydroxy-3-[(5-methyl-1-benzothiophen-2-yl)methoxy]cyclohex-2-ene-1-carboxylic acid
C17 H18 O6 S
BNUWPGVZRDEWEX-ISTRZQFTSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CB6 PDBBind:  2WKS Ki: 130 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.85α = 90
b = 157.85β = 90
c = 99.78γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-06-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-14
    Changes: Database references
  • Version 1.4: 2019-07-24
    Changes: Data collection