8E23 | pdb_00008e23

Human DNA polymerase theta in complex with allosteric inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8E23/pdb
• NAKB: 8E23

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli, synthetic construct
• Mutation(s): No 


• Deposited: 2022-08-13 Released: 2022-09-28 
• Deposition Author(s): Mader, P., Pau, V.P.T., Sicheri, F.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.295 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

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

• PubMed: 36126059 
• DOI: https://doi.org/10.1021/acs.jmedchem.2c00998
• Primary Citation 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.

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Organizational Affiliation: 
• Repare Therapeutics, 7171 Frederick-Banting, Building 2, Montréal, Québec H4S 1Z9, Canada.
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada.
Department of Chemistry and Chemical Biology, NE-CAT, Argonne, Cornell University, Illinois, New York 60439, United States.
Ventus Therapeutics, 7150 Frederick-Banting Suite 200, Montréal, Québec H4S 2A1, Canada.
Paraza Pharma Inc., 2525 Ave. Marie Curie, Montréal, Québec H4S 1Z9, Canada.
National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec H4P 2R2, Canada.
Piramal Pharma Ltd., Plot No. 18, Village Matoda, Taluka: Sanand, Ahmedabad, Gujarat 382213, India.
Molecular Biology Program, Sloan Kettering Institute, MSKCC, 430 E 67th Street, New York, New York 10065, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 170.08 kDa 
• Atom Count: 10,562 
• Modeled Residue Count: 1,286 
• Deposited Residue Count: 1,396 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase theta	A, D	668	Homo sapiens	Mutation(s): 0  Gene Names: POLQ, POLH 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 ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')	B, E	17	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*C*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')	C, F	13	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DG3	H [auth A], K [auth D]	2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O12 P3 HDRRAMINWIWTNU-NTSWFWBYSA-N
UAF (Subject of Investigation/LOI)	I [auth A]	N-methyl-N-phenyl[(3aM)-3-(trifluoromethyl)cyclopenta[c]pyrazol-2(1H)-yl]ethanethioamide C16 H14 F3 N3 S HKIQFXYWIJQJAT-UHFFFAOYSA-N
MG	G [auth A], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.295 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 246.85	α = 90
b = 69.32	β = 122.55
c = 147.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-28 
Deposition Author(s): Mader, P., Pau, V.P.T., Sicheri, F.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	FDN 143277
Other private		--

Revision History  

• 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