6XTW | pdb_00006xtw

HumRadA33F in complex with peptidic inhibitor 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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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 RadA
A, B
231Pyrococcus furiosus DSM 3638Mutation(s): 22 
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.831α = 90
b = 89.831β = 90
c = 100.825γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NZWClick on this verticalbar to view details

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: 2021-03-24
    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