7ONT

PARP1 catalytic domain in complex with a selective pyridine carboxamide-based inhibitor (compound 22)

• PDB DOI: https://doi.org/10.2210/pdb7ONT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-05-25 Released: 2021-09-15 
• Deposition Author(s): Schimpl, M., Balazs, A., Barratt, D., Bista, M., Chuba, M., Degorce, S.L., Di Fruscia, P., Embrey, K., Ghosh, A., Gill, S., Gunnarsson, A., Hande, S., Hemsley, P., Heightman, T.D., Illuzzi, G., Lane, J., Larner, C., Leo, E., Madin, A., Martin, S., McWilliams, L., Orme, J., Pachl, F., Packer, M.J., Pike, A., Staniszewska, A.D., Talbot, V., Underwood, E., Varnes, G.J., Zhang, A., Zheng, X., Johannes, J.W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.244 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Literature

Discovery of 5-{4-[(7-Ethyl-6-oxo-5,6-dihydro-1,5-naphthyridin-3-yl)methyl]piperazin-1-yl}- N -methylpyridine-2-carboxamide (AZD5305): A PARP1-DNA Trapper with High Selectivity for PARP1 over PARP2 and Other PARPs.

Johannes, J.W., Balazs, A., Barratt, D., Bista, M., Chuba, M.D., Cosulich, S., Critchlow, S.E., Degorce, S.L., Di Fruscia, P., Edmondson, S.D., Embrey, K., Fawell, S., Ghosh, A., Gill, S.J., Gunnarsson, A., Hande, S.M., Heightman, T.D., Hemsley, P., Illuzzi, G., Lane, J., Larner, C., Leo, E., Liu, L., Madin, A., Martin, S., McWilliams, L., O'Connor, M.J., Orme, J.P., Pachl, F., Packer, M.J., Pei, X., Pike, A., Schimpl, M., She, H., Staniszewska, A.D., Talbot, V., Underwood, E., Varnes, J.G., Xue, L., Yao, T., Zhang, K., Zhang, A.X., Zheng, X.

(2021) J Med Chem 64: 14498-14512

• PubMed: 34570508 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c01012
• Primary Citation of Related Structures:  
  7ONR, 7ONS, 7ONT


• PubMed Abstract: 
  

  Poly-ADP-ribose-polymerase (PARP) inhibitors have achieved regulatory approval in oncology for homologous recombination repair deficient tumors including BRCA mutation. However, some have failed in combination with first-line chemotherapies, usually due to overlapping hematological toxicities. Currently approved PARP inhibitors lack selectivity for PARP1 over PARP2 and some other 16 PARP family members, and we hypothesized that this could contribute to toxicity. Recent literature has demonstrated that PARP1 inhibition and PARP1-DNA trapping are key for driving efficacy in a BRCA mutant background. Herein, we describe the structure- and property-based design of 25 (AZD5305), a potent and selective PARP1 inhibitor and PARP1-DNA trapper with excellent in vivo efficacy in a BRCA mutant HBCx-17 PDX model. Compound 25 is highly selective for PARP1 over other PARP family members, with good secondary pharmacology and physicochemical properties and excellent pharmacokinetics in preclinical species, with reduced effects on human bone marrow progenitor cells in vitro.

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Organizational Affiliation: 

Chemistry, Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79.63 kDa 
• Atom Count: 6,006 
• Modelled Residue Count: 700 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 1	A, B	352	Homo sapiens	Mutation(s): 1  Gene Names: PARP1, ADPRT, PPOL EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P09874 (Homo sapiens) Explore P09874  Go to UniProtKB:  P09874
PHAROS:  P09874 GTEx:  ENSG00000143799

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VKQ (Subject of Investigation/LOI)	C [auth A], E [auth B]	5-[4-[(3-ethyl-2-oxidanylidene-1~{H}-quinolin-7-yl)methyl]piperazin-1-yl]-~{N}-methyl-pyridine-2-carboxamide C23 H27 N5 O2 CEIZJAXIHJZKRG-UHFFFAOYSA-N
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.244 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.573	α = 90
b = 92.621	β = 90
c = 164.312	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
STARANISO	data scaling
AMoRE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Schimpl, M., Balazs, A., Barratt, D., Bista, M., Chuba, M., Degorce, S.L., Di Fruscia, P., Embrey, K., Ghosh, A., Gill, S., Gunnarsson, A., Hande, S., Hemsley, P., Heightman, T.D., Illuzzi, G., Lane, J., Larner, C., Leo, E., Madin, A., Martin, S., McWilliams, L., Orme, J., Pachl, F., Packer, M.J., Pike, A., Staniszewska, A.D., Talbot, V., Underwood, E., Varnes, G.J., Zhang, A., Zheng, X., Johannes, J.W.

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Funding Organization	Location	Grant Number
Not funded	United Kingdom	--

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2021-10-13
  Changes: Data collection, Database references
• Version 1.2: 2021-10-27
  Changes: Data collection, Database references