4IJH

Fragment-based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

wwPDB Validation 3D Report Full Report



Literature

Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A.

Patrone, J.D.Kennedy, J.P.Frank, A.O.Feldkamp, M.D.Vangamudi, B.Pelz, N.F.Rossanese, O.W.Waterson, A.G.Chazin, W.J.Fesik, S.W.

(2013) ACS Med Chem Lett 4: 601-605

  • DOI: 10.1021/ml400032y
  • Primary Citation of Related Structures:  
    4IJH, 4IJL

  • PubMed Abstract: 
  • Replication Protein A (RPA) is a ssDNA binding protein that is essential for DNA replication and repair. The initiation of the DNA damage response by RPA is mediated by protein-protein interactions involving the N-terminal domain of the 70 kDa subunit with partner proteins ...

    Replication Protein A (RPA) is a ssDNA binding protein that is essential for DNA replication and repair. The initiation of the DNA damage response by RPA is mediated by protein-protein interactions involving the N-terminal domain of the 70 kDa subunit with partner proteins. Inhibition of these interactions increases sensitivity towards DNA damage and replication stress and may therefore be a potential strategy for cancer drug discovery. Towards this end, we have discovered two lead series of compounds, derived from hits obtained from a fragment-based screen, that bind to RPA70N with low micromolar affinity and inhibit the binding of an ATRIP-derived peptide to RPA. These compounds may offer a promising starting point for the discovery of clinically useful RPA inhibitors.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232 (USA).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replication protein A 70 kDa DNA-binding subunitA123Homo sapiensMutation(s): 1 
Gene Names: REPA1RPA1RPA70
Find proteins for P27694 (Homo sapiens)
Explore P27694 
Go to UniProtKB:  P27694
NIH Common Fund Data Resources
PHAROS  P27694
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1EJ
Query on 1EJ

Download CCD File 
A
3-chloro-6-[3-(4-fluorophenyl)-5-sulfanyl-4H-1,2,4-triazol-4-yl]-1-benzothiophene-2-carboxylic acid
C17 H9 Cl F N3 O2 S2
PNSKQUARDFXFAX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1EJKd :  47000   nM  PDBBind
1EJKd:  47000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.871α = 90
b = 52.629β = 90
c = 54.518γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-14
    Type: Initial release