4O0A

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    4O0A, 4LUV, 4LUZ, 4LUO, 4LW1, 4LWC

  • 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 and repair ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replication protein A 70 kDa DNA-binding subunitA123Homo sapiensMutation(s): 1 
Gene Names: RPA1REPA1RPA70
Find proteins for P27694 (Homo sapiens)
Explore P27694 
Go to UniProtKB:  P27694
NIH Common Fund Data Resources
PHAROS:  P27694
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2P9
Query on 2P9

Download Ideal Coordinates CCD File 
B [auth A]5-{4-[({[4-(5-carboxyfuran-2-yl)-2-chlorophenyl]carbonothioyl}amino)methyl]phenyl}-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid
C29 H18 Cl3 N3 O5 S
RSWLTGWUCSWTHA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2P9Kd:  290   nM  BindingDB
2P9Kd:  2300   nM  BindingDB
2P9Kd:  323   nM  BindingDB
2P9Kd:  5200   nM  BindingDB
2P9Kd:  190   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.912α = 90
b = 53.582β = 90
c = 53.932γ = 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  (Full details and data files)

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Structure summary
  • Version 1.2: 2018-10-10
    Changes: Data collection, Database references, Structure summary