Structure of a small molecule inhibitor bound to a DNA sliding clamp

Experimental Data Snapshot

  • Resolution: 1.64 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.256 

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Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp.

Georgescu, R.E.Yurieva, O.Kim, S.S.Kuriyan, J.Kong, X.P.O'Donnell, M.

(2008) Proc Natl Acad Sci U S A 105: 11116-11121

  • DOI: https://doi.org/10.1073/pnas.0804754105
  • Primary Citation of Related Structures:  
    3D1E, 3D1F, 3D1G

  • PubMed Abstract: 

    DNA polymerases attach to the DNA sliding clamp through a common overlapping binding site. We identify a small-molecule compound that binds the protein-binding site in the Escherichia coli beta-clamp and differentially affects the activity of DNA polymerases II, III, and IV. To understand the molecular basis of this discrimination, the cocrystal structure of the chemical inhibitor is solved in complex with beta and is compared with the structures of Pol II, Pol III, and Pol IV peptides bound to beta. The analysis reveals that the small molecule localizes in a region of the clamp to which the DNA polymerases attach in different ways. The results suggest that the small molecule may be useful in the future to probe polymerase function with beta, and that the beta-clamp may represent an antibiotic target.

  • Organizational Affiliation

    The Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, P. O. Box 228, New York, NY 10065, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase III subunit beta
A, B
366Escherichia coliMutation(s): 0 
Gene Names: dnaN
Find proteins for P0A988 (Escherichia coli (strain K12))
Explore P0A988 
Go to UniProtKB:  P0A988
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A988
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 322

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
[(5R)-5-(2,3-dibromo-5-ethoxy-4-hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid
C14 H13 Br2 N O5 S2
Binding Affinity Annotations 
IDSourceBinding Affinity
322 PDBBind:  3D1G Ki: 1.00e+4 (nM) from 1 assay(s)
Binding MOAD:  3D1G Ki: 1.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.64 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.256 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.72α = 110.24
b = 79.395β = 100.58
c = 80.505γ = 99.46
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description