4IJL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  

  • 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 subuni ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replication protein A 70 kDa DNA-binding subunit
A
123Homo sapiensMutation(s): 1 
Gene Names: RPA1 (REPA1, RPA70)
Find proteins for P27694 (Homo sapiens)
Go to Gene View: RPA1
Go to UniProtKB:  P27694
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1EK
Query on 1EK

Download SDF File 
Download CCD File 
A
{[5-(3-chloro-1-benzothiophen-2-yl)-4-phenyl-4H-1,2,4-triazol-3-yl]sulfanyl}acetic acid
C18 H12 Cl N3 O2 S2
GNEUDTMFXMASKC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1EKKd: 135000 nM BINDINGMOAD
1EKKd: 135000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.551α = 90.00
b = 53.569β = 90.00
c = 54.259γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data collection
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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