9D6N | pdb_00009d6n

Loop-Deleted DNA Polymerase Theta in Complex with a dsDNA Overhang and an Allostertic Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.237 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

RTx-303, an Orally Bioavailable Pol theta Polymerase Inhibitor That Potentiates PARP Inhibitors in BRCA Mutant Tumors.

Chandramouly, G.Fried, W.Gordon, J.Ralph, D.Keuk, C.Kumari, S.Ramanjulu, M.Auerbacher, W.Minakhin, L.Tredinnick, T.Tiberi, B.Morton, G.Betsch, R.Cai, K.Q.Vekariya, U.M.Tyagi, M.Skorski, T.Karakashev, S.Johnson, N.Childers Jr., W.E.Chen, X.S.Pomerantz, R.T.

(2025) J Med Chem 68: 22196-22215

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00551
  • Primary Citation of Related Structures:  
    9D6N, 9D6O

  • PubMed Abstract: 

    DNA polymerase θ (Polθ) is a polymerase-helicase fusion protein that is synthetically lethal with homologous recombination (HR) factors, such as BRCA1/2, and confers resistance to PARP inhibitors (PARPi) and other genotoxic cancer therapies. Previously developed Polθ polymerase (Polθ-pol) inhibitors (Polθi) exhibited limited pharmacological activity and metabolic stability, warranting the development of a Polθi with improved drug-like properties. Here, we developed RTx-303, a selective allosteric small-molecule Polθ-pol inhibitor that exhibits 5.1 nM IC 50 , 88% oral bioavailability, and a prolonged half-life along with its equipotent metabolite. X-ray crystallography highlights the development of a solvent-exposed side-chain that is essential for the optimal drug-like properties of RTx-303. Notably, RTx-303 exhibits significantly higher cellular potency than previously developed Polθ-pol inhibitors and strongly potentiates PARPi in BRCA1/2 mutant cells and patient-derived xenograft models. The superior potency, robust pharmacological activity, and high tolerability of RTx-303 warrant further development as a Polθ-pol inhibitor drug candidate.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase thetaA,
D [auth B]
652Homo sapiensMutation(s): 0 
Gene Names: POLQPOLH
EC: 3.6.4.12 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 2.7.7.49 (PDB Primary Data)
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
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA TemplateB [auth E],
E [auth C]
24synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA PrimerC [auth F],
F [auth D]
14synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A2C (Subject of Investigation/LOI)
Query on A1A2C

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B]
2-{3-[(2R)-3-(dimethylamino)-2-hydroxypropyl]-2-oxoimidazolidin-1-yl}-4,6-bis(trifluoromethyl)phenyl (4-fluorophenyl)(methyl)carbamate
C24 H25 F7 N4 O4
XOWJYFCVFGFEFB-UHFFFAOYSA-N
DG3
Query on DG3

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B]
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
HDRRAMINWIWTNU-NTSWFWBYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.237 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.119α = 90
b = 171.119β = 90
c = 118.026γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Cootmodel building
DIALSdata reduction
DIALSdata scaling
BOSdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM130889

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release
  • Version 1.1: 2026-03-04
    Changes: Database references