6TW3

HumRadA2 in complex with Naphthyl-HPA fragment-peptide chimera


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A small-molecule inhibitor of the BRCA2-RAD51 interaction modulates RAD51 assembly and potentiates DNA damage-induced cell death.

Scott, D.E.Francis-Newton, N.J.Marsh, M.E.Coyne, A.G.Fischer, G.Moschetti, T.Bayly, A.R.Sharpe, T.D.Haas, K.T.Barber, L.Valenzano, C.R.Srinivasan, R.Huggins, D.J.Lee, M.Emery, A.Hardwick, B.Ehebauer, M.Dagostin, C.Esposito, A.Pellegrini, L.Perrior, T.McKenzie, G.Blundell, T.L.Hyvonen, M.Skidmore, J.Venkitaraman, A.R.Abell, C.

(2021) Cell Chem Biol 28: 835

  • DOI: https://doi.org/10.1016/j.chembiol.2021.02.006
  • Primary Citation of Related Structures:  
    6TV3, 6TW3, 6TW4, 6TW9, 6XTW

  • PubMed Abstract: 

    BRCA2 controls RAD51 recombinase during homologous DNA recombination (HDR) through eight evolutionarily conserved BRC repeats, which individually engage RAD51 via the motif Phe-x-x-Ala. Using structure-guided molecular design, templated on a monomeric thermostable chimera between human RAD51 and archaeal RadA, we identify CAM833, a 529 Da orthosteric inhibitor of RAD51:BRC with a K d of 366 nM. The quinoline of CAM833 occupies a hotspot, the Phe-binding pocket on RAD51 and the methyl of the substituted α-methylbenzyl group occupies the Ala-binding pocket. In cells, CAM833 diminishes formation of damage-induced RAD51 nuclear foci; inhibits RAD51 molecular clustering, suppressing extended RAD51 filament assembly; potentiates cytotoxicity by ionizing radiation, augmenting 4N cell-cycle arrest and apoptotic cell death and works with poly-ADP ribose polymerase (PARP)1 inhibitors to suppress growth in BRCA2-wildtype cells. Thus, chemical inhibition of the protein-protein interaction between BRCA2 and RAD51 disrupts HDR and potentiates DNA damage-induced cell death, with implications for cancer therapy.


  • Organizational Affiliation

    Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair and recombination protein RadA231Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: radAPF1926
UniProt
Find proteins for O74036 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore O74036 
Go to UniProtKB:  O74036
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74036
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O0E (Subject of Investigation/LOI)
Query on O0E

Download Ideal Coordinates CCD File 
D [auth A](2~{S})-1-[(2~{S})-2-[(3-azanylnaphthalen-2-yl)carbonylamino]-3-(1~{H}-imidazol-4-yl)propanoyl]-~{N}-[(2~{S})-1-azanyl-1-oxidanylidene-propan-2-yl]pyrrolidine-2-carboxamide
C25 H29 N7 O4
ZPEDIFPSGYUDLA-WVFSVQOHSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.526α = 90
b = 61.949β = 90
c = 87.724γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom91050/Z/10/Z
Wellcome TrustUnited Kingdom080083/Z/06/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2021-06-30
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description