4N99

E. coli sliding clamp in complex with 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-7-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of lead compounds targeting the bacterial sliding clamp using a fragment-based approach.

Yin, Z.Whittell, L.R.Wang, Y.Jergic, S.Liu, M.Harry, E.J.Dixon, N.E.Beck, J.L.Kelso, M.J.Oakley, A.J.

(2014) J Med Chem 57: 2799-2806

  • DOI: 10.1021/jm500122r
  • Primary Citation of Related Structures:  
    4N97, 4N98, 4N99, 4N94, 4N95, 4N96, 4N9A

  • PubMed Abstract: 
  • The bacterial sliding clamp (SC), also known as the DNA polymerase III β subunit, is an emerging antibacterial target that plays a central role in DNA replication, serving as a protein-protein interaction hub with a common binding pocket to recognize linear motifs in the partner proteins ...

    The bacterial sliding clamp (SC), also known as the DNA polymerase III β subunit, is an emerging antibacterial target that plays a central role in DNA replication, serving as a protein-protein interaction hub with a common binding pocket to recognize linear motifs in the partner proteins. Here, fragment-based screening using X-ray crystallography produced four hits bound in the linear-motif-binding pocket of the Escherichia coli SC. Compounds structurally related to the hits were identified that inhibited the E. coli SC and SC-mediated DNA replication in vitro. A tetrahydrocarbazole derivative emerged as a promising lead whose methyl and ethyl ester prodrug forms showed minimum inhibitory concentrations in the range of 21-43 μg/mL against representative Gram-negative and Gram-positive bacteria species. The work demonstrates the utility of a fragment-based approach for identifying bacterial sliding clamp inhibitors as lead compounds with broad-spectrum antibacterial activity.


    Organizational Affiliation

    School of Chemistry and Centre for Medical and Molecular Bioscience, University of Wollongong , Wollongong, New South Wales 2522, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III subunit betaA, B366Escherichia coli K-12Mutation(s): 0 
Gene Names: b3701dnaNJW3678
EC: 2.7.7.7
Find proteins for P0A988 (Escherichia coli (strain K12))
Explore P0A988 
Go to UniProtKB:  P0A988
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2J1
Query on 2J1

Download Ideal Coordinates CCD File 
C [auth A]6-chloro-2,3,4,9-tetrahydro-1H-carbazole-7-carboxylic acid
C13 H12 Cl N O2
QPXAEUZWZDSOOF-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
EA [auth B] , F [auth A] , FA [auth B] , L [auth A] , Q [auth A] , R [auth A] , U [auth B] , V [auth B] , 
EA [auth B],  F [auth A],  FA [auth B],  L [auth A],  Q [auth A],  R [auth A],  U [auth B],  V [auth B],  X [auth B],  Z [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , CA [auth B] , D [auth A] , DA [auth B] , E [auth A] , G [auth A] , GA [auth B] , 
AA [auth B],  BA [auth B],  CA [auth B],  D [auth A],  DA [auth B],  E [auth A],  G [auth A],  GA [auth B],  H [auth A],  HA [auth B],  IA [auth B],  J [auth A],  JA [auth B],  N [auth A],  O [auth A],  P [auth A],  T [auth A],  W [auth B],  Y [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
I [auth A], K [auth A], KA [auth B], M [auth A], S [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2J1Ki:  216000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.265 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.01α = 72.95
b = 65.13β = 85.06
c = 73.24γ = 85.24
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-10-19 
  • Released Date: 2013-11-06 
  • Deposition Author(s): Yin, Z., Oakley, A.J.

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2014-04-02
    Changes: Database references
  • Version 1.2: 2014-04-09
    Changes: Database references