8E23

Human DNA polymerase theta in complex with allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification of RP-6685 , an Orally Bioavailable Compound that Inhibits the DNA Polymerase Activity of Pol theta.

Bubenik, M.Mader, P.Mochirian, P.Vallee, F.Clark, J.Truchon, J.F.Perryman, A.L.Pau, V.Kurinov, I.Zahn, K.E.Leclaire, M.E.Papp, R.Mathieu, M.C.Hamel, M.Duffy, N.M.Godbout, C.Casas-Selves, M.Falgueyret, J.P.Baruah, P.S.Nicolas, O.Stocco, R.Poirier, H.Martino, G.Fortin, A.B.Roulston, A.Chefson, A.Dorich, S.St-Onge, M.Patel, P.Pellerin, C.Ciblat, S.Pinter, T.Barabe, F.El Bakkouri, M.Parikh, P.Gervais, C.Sfeir, A.Mamane, Y.Morris, S.J.Black, W.C.Sicheri, F.Gallant, M.

(2022) J Med Chem 65: 13198-13215

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00998
  • Primary Citation of Related Structures:  
    8E23, 8E24

  • PubMed Abstract: 

    DNA polymerase theta (Polθ) is an attractive synthetic lethal target for drug discovery, predicted to be efficacious against breast and ovarian cancers harboring BRCA-mutant alleles. Here, we describe our hit-to-lead efforts in search of a selective inhibitor of human Polθ (encoded by POLQ). A high-throughput screening campaign of 350,000 compounds identified an 11 micromolar hit, giving rise to the N2-substituted fused pyrazolo series, which was validated by biophysical methods. Structure-based drug design efforts along with optimization of cellular potency and ADME ultimately led to the identification of RP-6685 : a potent, selective, and orally bioavailable Polθ inhibitor that showed in vivo efficacy in an HCT116 BRCA2 -/- mouse tumor xenograft model.


  • Organizational Affiliation

    Repare Therapeutics, 7171 Frederick-Banting, Building 2, Montréal, Québec H4S 1Z9, Canada.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase theta
A, D
668Homo sapiensMutation(s): 0 
Gene Names: POLQPOLH
EC: 2.7.7.7 (PDB Primary Data), 3.6.4.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75417 (Homo sapiens)
Explore O75417 
Go to UniProtKB:  O75417
PHAROS:  O75417
GTEx:  ENSG00000051341 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75417
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
B, E
17synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*C*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
C, F
13synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 246.85α = 90
b = 69.32β = 122.55
c = 147.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaFDN 143277
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description