5FXT

Crystal Structure of Helicobacter pylori beta clamp in complex with Carprofen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Screening of E. coli beta-clamp Inhibitors Revealed that Few Inhibit Helicobacter pylori More Effectively: Structural and Functional Characterization.

Pandey, P.Verma, V.Dhar, S.K.Gourinath, S.

(2018) Antibiotics (Basel) 7

  • DOI: https://doi.org/10.3390/antibiotics7010005
  • Primary Citation of Related Structures:  
    5FVE, 5FXT, 5G4Q

  • PubMed Abstract: 

    The characteristic of interaction with various enzymes and processivity-promoting nature during DNA replication makes β-clamp an important drug target. Helicobacter pylori ( H. pylori ) have several unique features in DNA replication machinery that makes it different from other microorganisms. To find out whether difference in DNA replication proteins behavior accounts for any difference in drug response when compared to E. coli , in the present study, we have tested E. coli β-clamp inhibitor molecules against H. pylori β-clamp. Various approaches were used to test the binding of inhibitors to H. pylori β-clamp including docking, surface competition assay, complex structure determination, as well as antimicrobial assay. Out of five shortlisted inhibitor molecules on the basis of docking score, three molecules, 5-chloroisatin, carprofen, and 3,4-difluorobenzamide were co-crystallized with H. pylori β-clamp and the structures show that they bind at the protein-protein interaction site as expected. In vivo studies showed only two molecules, 5-chloroisatin, and 3,4-difluorobenzamide inhibited the growth of the pylori with MIC values in micro molar range, which is better than the inhibitory effect of the same drugs on E. coli . Therefore, the evaluation of such drugs against H. pylori may explore the possibility to use to generate species-specific pharmacophore for development of new drugs against H. pylori .


  • Organizational Affiliation

    School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India. preet.satya@gmail.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA POLYMERASE III SUBUNIT BETA374Helicobacter pylori 26695Mutation(s): 0 
EC: 2.7.7.7
UniProt
Find proteins for O25242 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25242 
Go to UniProtKB:  O25242
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25242
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0LA
Query on 0LA

Download Ideal Coordinates CCD File 
B [auth A](2S)-2-(6-chloro-9H-carbazol-2-yl)propanoic acid
C15 H12 Cl N O2
PUXBGTOOZJQSKH-QMMMGPOBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.921α = 90
b = 66.445β = 115.56
c = 82.867γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Database references
  • Version 1.2: 2021-03-03
    Changes: Derived calculations
  • Version 1.3: 2021-03-17
    Changes: Derived calculations
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description