Structure of Helicobacter pylori type II dehydroquinase in complex with inhibitor compound (2R)-2-(4-methoxybenzyl)-3-dehydroquinic acid

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

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This is version 1.5 of the entry. See complete history


Understanding the Key Factors that Control the Inhibition of Type II Dehydroquinase by (2R)-2- Benzyl-3-Dehydroquinic Acids.

Peon, A.Otero, J.M.Tizon, L.Prazeres, V.F.V.Llamas-Saiz, A.L.Fox, G.C.van Raaij, M.J.Lamb, H.Hawkins, A.R.Gago, F.Castedo, L.Gonzalez-Bello, C.

(2010) ChemMedChem 5: 1726

  • DOI: https://doi.org/10.1002/cmdc.201000281
  • Primary Citation of Related Structures:  
    2XB8, 2XB9

  • PubMed Abstract: 

    The binding mode of several substrate analogues, (2R)-2-benzyl-3-dehydroquinic acids 4, which are potent reversible competitive inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway, has been investigated by structural and computational studies. The crystal structures of Mycobacterium tuberculosis and Helicobacter pylori DHQ2 in complex with one of the most potent inhibitor, p-methoxybenzyl derivative 4 a, have been solved at 2.40 Å and 2.75 Å, respectively. This has allowed the resolution of the M. tuberculosis DHQ2 loop containing residues 20-25 for the first time. These structures show the key interactions of the aromatic ring in the active site of both enzymes and additionally reveal an important change in the conformation and flexibility of the loop that closes over substrate binding. The loop conformation and the binding mode of compounds 4 b-d has been also studied by molecular dynamics simulations, which suggest that the benzyl group of inhibitors 4 prevent appropriate orientation of the catalytic tyrosine of the loop for proton abstraction and disrupts its basicity.

  • Organizational Affiliation

    Departamento de Química Orgánica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
167Helicobacter pyloriMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on XNW

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
C15 H18 O7
Query on CIT

Download Ideal Coordinates CCD File 
C6 H8 O7
Binding Affinity Annotations 
IDSourceBinding Affinity
XNW PDBBind:  2XB9 Ki: 170 (nM) from 1 assay(s)
CIT BindingDB:  2XB9 Kd: 2500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.75 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 42 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.56α = 90
b = 100.56β = 90
c = 105.449γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2018-02-07
    Changes: Database references
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description