5E7N

Crystal Structure of RPA70N in complex with VU0085636


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification and Optimization of Anthranilic Acid Based Inhibitors of Replication Protein A.

Patrone, J.D.Pelz, N.F.Bates, B.S.Souza-Fagundes, E.M.Vangamudi, B.Camper, D.V.Kuznetsov, A.G.Browning, C.F.Feldkamp, M.D.Frank, A.O.Gilston, B.A.Olejniczak, E.T.Rossanese, O.W.Waterson, A.G.Chazin, W.J.Fesik, S.W.

(2016) Chemmedchem 11: 893-899

  • DOI: 10.1002/cmdc.201500479

  • PubMed Abstract: 
  • Replication protein A (RPA) is an essential single-stranded DNA (ssDNA)-binding protein that initiates the DNA damage response pathway through protein-protein interactions (PPIs) mediated by its 70N domain. The identification and use of chemical prob ...

    Replication protein A (RPA) is an essential single-stranded DNA (ssDNA)-binding protein that initiates the DNA damage response pathway through protein-protein interactions (PPIs) mediated by its 70N domain. The identification and use of chemical probes that can specifically disrupt these interactions is important for validating RPA as a cancer target. A high-throughput screen (HTS) to identify new chemical entities was conducted, and 90 hit compounds were identified. From these initial hits, an anthranilic acid based series was optimized by using a structure-guided iterative medicinal chemistry approach to yield a cell-penetrant compound that binds to RPA70N with an affinity of 812 nm. This compound, 2-(3- (N-(3,4-dichlorophenyl)sulfamoyl)-4-methylbenzamido)benzoic acid (20 c), is capable of inhibiting PPIs mediated by this domain.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University, 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
5KR
Query on 5KR

Download SDF File 
Download CCD File 
A
2-({3-[(4-bromophenyl)sulfamoyl]-4-methylbenzoyl}amino)benzoic acid
C21 H17 Br N2 O5 S
UMIZGACLAWLSMJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.560α = 90.00
b = 53.260β = 90.00
c = 54.480γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM065484
National Institutes of Health/National Cancer InstituteUnited States5DP1OD006933/8DP1CA174419

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-05-04
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations