Crystal Structure of RPA70N in complex with VU0085636

Experimental Data Snapshot

  • Resolution: 1.21 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

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This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1002/cmdc.201500479
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replication protein A 70 kDa DNA-binding subunit123Homo sapiensMutation(s): 1 
Gene Names: RPA1REPA1RPA70
UniProt & NIH Common Fund Data Resources
Find proteins for P27694 (Homo sapiens)
Explore P27694 
Go to UniProtKB:  P27694
PHAROS:  P27694
GTEx:  ENSG00000132383 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27694
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5KR

Download Ideal Coordinates CCD File 
B [auth A]2-({3-[(4-bromophenyl)sulfamoyl]-4-methylbenzoyl}amino)benzoic acid
C21 H17 Br N2 O5 S
Binding Affinity Annotations 
IDSourceBinding Affinity
5KR Binding MOAD:  5E7N Kd: 3.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.21 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.56α = 90
b = 53.26β = 90
c = 54.48γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM065484
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5DP1OD006933/8DP1CA174419

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description