5G48 | pdb_00005g48

H.pylori Beta clamp in complex with Diflunisal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.255 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5G48

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Targeting the beta-clamp in Helicobacter pylori with FDA-approved drugs reveals micromolar inhibition by diflunisal.

Pandey, P.Verma, V.Gautam, G.Kumari, N.Dhar, S.K.Gourinath, S.

(2017) FEBS Lett 591: 2311-2322

  • DOI: https://doi.org/10.1002/1873-3468.12734
  • Primary Citation Related Structures: 
    5G48

  • PubMed Abstract: 

    The β-clamp is the processivity-promoting factor for most of the enzymes in prokaryotic DNA replication; hence, it is a crucial drug target. In the present study, we investigated the β-clamp from Helicobacter pylori, aiming to seek potential drug molecules against this gastric-cancer-causing bacterium. An in silico screening of Food and Drug Administration (FDA) approved drugs against the H. pylori β-clamp, followed by its in vitro inhibition using a surface competition approach, yielded the drug diflunisal as a positive initial hit. Diflunisal inhibits the growth of H. pylori in the micromolar range. We determined the structure of diflunisal in complex with the β-clamp to show that the drug binds at subsite I, which is a protein-protein interaction site. Successful identification of FDA-approved molecules against H. pylori may lead to better and faster drug development.


  • Organizational Affiliation
    • School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.

Macromolecule Content 

  • Total Structure Weight: 84.98 kDa 
  • Atom Count: 6,057 
  • Modeled Residue Count: 744 
  • Deposited Residue Count: 748 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA POLYMERASE III SUBUNIT BETA
A, B
374Helicobacter pylori 26695Mutation(s): 0 
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.255 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.311α = 90
b = 66.372β = 115.96
c = 89.119γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description