9ETQ

Crystal structure of PARP1 catalytic domain bound to AZD5305 (SARUPARIB)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of 6-Fluoro-5-{4-[(5-fluoro-2-methyl-3-oxo-3,4-dihydroquinoxalin-6-yl)methyl]piperazin-1-yl}- N -methylpyridine-2-carboxamide (AZD9574): A CNS-Penetrant, PARP1-Selective Inhibitor.

Johannes, J.W.Balazs, A.Y.S.Barratt, D.Bista, M.Chuba, M.D.Cosulich, S.Critchlow, S.E.Degorce, S.L.Di Fruscia, P.Edmondson, S.D.Embrey, K.J.Fawell, S.Ghosh, A.Gill, S.J.Gunnarsson, A.Hande, S.M.Heightman, T.D.Hemsley, P.Illuzzi, G.Lane, J.Larner, C.J.B.Leo, E.Liu, L.Madin, A.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.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01725
  • Primary Citation of Related Structures:  
    9ETQ, 9ETR

  • PubMed Abstract: 

    PARP inhibitors have attracted considerable interest in drug discovery due to the clinical success of first-generation agents such as olaparib, niraparib, rucaparib, and talazoparib. Their success lies in their ability to trap PARP to DNA; however, first-generation PARP inhibitors were not strictly optimized for trapping nor for selectivity among the PARP enzyme family. Previously we described the discovery of the second-generation PARP inhibitor AZD5305, a selective PARP1-DNA trapper. AZD5305 maintained the antitumor efficacy of first-generation PARP inhibitors while exhibiting lower hematological toxicity. Recently, there has been interest in central nervous system (CNS)-penetrant PARP inhibitors for CNS malignancies and other neurological conditions; however, AZD5305 is not CNS penetrant. Herein we describe the discovery and optimization of a series of CNS-penetrant, PARP1-selective inhibitors and PARP1-DNA trappers, culminating in the discovery of AZD9574, a compound that maintains the PARP1 selectivity of AZD5305 with improved permeability, reduced efflux, and increased CNS penetration.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1
A, B
352Homo sapiensMutation(s): 1 
Gene Names: PARP1ADPRTPPOL
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09874
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H63 (Subject of Investigation/LOI)
Query on A1H63

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
5-[4-[(7-ethyl-6-oxidanylidene-5~{H}-1,5-naphthyridin-3-yl)methyl]piperazin-1-yl]-~{N}-methyl-pyridine-2-carboxamide
C22 H26 N6 O2
WQAVGRAETZEADU-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.234α = 90
b = 92.535β = 90
c = 163.544γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
STARANISOdata scaling
XDSdata reduction
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-12-04 
  • Deposition Author(s): Schimpl, M.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Database references