Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Tetrahedral - T  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 113.10 kDa 
• Atom Count: 7257 
• Modelled Residue Count: 918 
• Deposited Residue Count: 1002 
• Unique protein chains: 1

2WKS

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

• DOI: 10.2210/pdb2WKS/pdb

• Classification: LYASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-06-17 Released: 2009-11-24 
• Deposition Author(s): Otero, J.M., Guardado-Calvo, P., Llamas-Saiz, A.L., Prazeres, V.F.V., Tizon, L., Castedo, L., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

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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 

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

• PubMed: 19911771 
• 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. 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.

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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

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B, C, D, E, F	167	Helicobacter pylori	Mutation(s): 0  EC: 4.2.1.10
UniProt
Find proteins for Q48255 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore Q48255  Go to UniProtKB:  Q48255

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CB6 (Subject of Investigation/LOI)	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

Binding Affinity Annotations
ID	Source	Binding 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 = 157.85	α = 90
b = 157.85	β = 90
c = 99.78	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2009-06-17 
• Released Date: 2009-11-24 
Deposition Author(s): Otero, J.M., Guardado-Calvo, P., Llamas-Saiz, A.L., Prazeres, V.F.V., Tizon, L., Castedo, L., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

Revision History  

• 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