8E24 | pdb_00008e24

Human DNA polymerase theta in complex with allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 
    0.266 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UA6Click on this verticalbar to view details

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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DG3
Query on DG3

Download Ideal Coordinates CCD File 
H [auth A],
K [auth D]
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
HDRRAMINWIWTNU-NTSWFWBYSA-N
UA6 (Subject of Investigation/LOI)
Query on UA6

Download Ideal Coordinates CCD File 
I [auth A],
L [auth D]
2-[2,4-bis(trifluoromethyl)phenyl]-N-phenyl-N-[3-(pyridazin-3-yl)prop-2-yn-1-yl]acetamide
C23 H15 F6 N3 O
SCSRPWBBDHKGCX-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
J [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UA6 BindingDB:  8E24 IC50: 1.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free:  0.266 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 263.739α = 90
b = 66.287β = 126.14
c = 156.662γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

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 UA6Click on this verticalbar to view details

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