4LWC

Fragment-Based Discovery of a Potent Inhibitor of Replication Protein A Protein-Protein Interactions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery of a potent inhibitor of replication protein a protein-protein interactions using a fragment-linking approach.

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

(2013) J.Med.Chem. 56: 9242-9250

  • DOI: 10.1021/jm401333u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Replication protein A (RPA), the major eukaryotic single-stranded DNA (ssDNA)-binding protein, is involved in nearly all cellular DNA transactions. The RPA N-terminal domain (RPA70N) is a recruitment site for proteins involved in DNA-damage response ...

    Replication protein A (RPA), the major eukaryotic single-stranded DNA (ssDNA)-binding protein, is involved in nearly all cellular DNA transactions. The RPA N-terminal domain (RPA70N) is a recruitment site for proteins involved in DNA-damage response and repair. Selective inhibition of these protein-protein interactions has the potential to inhibit the DNA-damage response and to sensitize cancer cells to DNA-damaging agents without affecting other functions of RPA. To discover a potent, selective inhibitor of the RPA70N protein-protein interactions to test this hypothesis, we used NMR spectroscopy to identify fragment hits that bind to two adjacent sites in the basic cleft of RPA70N. High-resolution X-ray crystal structures of RPA70N-ligand complexes revealed how these fragments bind to RPA and guided the design of linked compounds that simultaneously occupy both sites. We have synthesized linked molecules that bind to RPA70N with submicromolar affinity and minimal disruption of RPA's interaction with ssDNA.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States.




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
1XU
Query on 1XU

Download SDF File 
Download CCD File 
A
5-[3-chloro-4-({4-[1-(3,4-dichlorophenyl)-1H-pyrazol-5-yl]benzyl}carbamothioyl)phenyl]furan-2-carboxylic acid
C28 H18 Cl3 N3 O3 S
XXQKNGSPGDXDMG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1XUKd: 190 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.208α = 90.00
b = 54.043β = 90.00
c = 54.356γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHENIXmodel building
PHENIXphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Database references
  • Version 1.2: 2014-12-10
    Type: Structure summary
  • Version 1.3: 2017-11-22
    Type: Advisory, Database references