4PNU

E. coli sliding clamp in complex with (R)-6-bromo-9-(2-((R)-1-carboxy-2-phenylethylamino)-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Bacterial Sliding Clamp Inhibitors that Mimic the Sequential Binding Mechanism of Endogenous Linear Motifs.

Yin, Z.Whittell, L.R.Wang, Y.Jergic, S.Ma, C.Lewis, P.J.Dixon, N.E.Beck, J.L.Kelso, M.J.Oakley, A.J.

(2015) J.Med.Chem. 58: 4693-4702

  • DOI: 10.1021/acs.jmedchem.5b00232
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The bacterial DNA replication machinery presents new targets for the development of antibiotics acting via novel mechanisms. One such target is the protein-protein interaction between the DNA sliding clamp and the conserved peptide linear motifs in D ...

    The bacterial DNA replication machinery presents new targets for the development of antibiotics acting via novel mechanisms. One such target is the protein-protein interaction between the DNA sliding clamp and the conserved peptide linear motifs in DNA polymerases. We previously established that binding of linear motifs to the Escherichia coli sliding clamp occurs via a sequential mechanism that involves two subsites (I and II). Here, we report the development of small-molecule inhibitors that mimic this mechanism. The compounds contain tetrahydrocarbazole moieties as "anchors" to occupy subsite I. Functional groups appended at the tetrahydrocarbazole nitrogen bind to a channel gated by the side chain of M362 and lie at the edge of subsite II. One derivative induced the formation of a new binding pocket, termed subsite III, by rearrangement of a loop adjacent to subsite I. Discovery of the extended binding area will guide further inhibitor development.


    Organizational Affiliation

    ‡School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia.,†School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit beta
A, B
366N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
2VD
Query on 2VD

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Download CCD File 
A, B
(2R)-6-bromo-9-(2-{[(1R)-1-carboxy-2-phenylethyl]amino}-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid
C24 H23 Br N2 O5
VVKCJZLVMZAHBK-DNVCBOLYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2VDIC50: 30000 nM (100) BINDINGDB
2VDKd: 13000 nM (100) BINDINGDB
2VDKi: 17000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.895α = 90.00
b = 67.193β = 114.54
c = 81.016γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
MAR345dtbdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-02-21 
  • Released Date: 2014-03-05 
  • Deposition Author(s): Yin, Z., Oakley, A.J.

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2015-06-24
    Type: Database references