8HE7

ADP-ribosyltransferase 1 (PARP1) catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

Discovery of Quinazoline-2,4(1 H ,3 H )-dione Derivatives Containing a Piperizinone Moiety as Potent PARP-1/2 Inhibitors─Design, Synthesis, In Vivo Antitumor Activity, and X-ray Crystal Structure Analysis.

Zhou, J.Du, T.Wang, X.Yao, H.Deng, J.Li, Y.Chen, X.Sheng, L.Ji, M.Xu, B.

(2023) J Med Chem 66: 14095-14115

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01152
  • Primary Citation of Related Structures:  
    8HE7, 8HE8

  • PubMed Abstract: 

    PARP-1/2 inhibitors have become an important therapeutic strategy for the treatment of HR-deficient tumors. However, discovery of new inhibitors with an improved and distinct pharmacological file still need enormous explorations. Herein, a series of novel highly potent PARP-1/2 inhibitors bearing an N -substituted piperazinone moiety were achieved. In particular, Cpd36 was identified as a distinct PARP inhibitor, showing remarkable enzymatic activity not only toward PARP-1 (IC 50 = 0.94 nM) and PARP-2 (IC 50 = 0.87 nM) but also toward PARP-7 (IC 50 = 0.21 nM), as well as high selectivity over other PARP isoforms. Furthermore, Cpd36 was orally bioavailable and significantly repressed the tumor growth in both breast cancer and prostate cancer xenograft model. The crystal structures of Cpd36 within PARP-1 and PARP-2 together with the predicted binding mode within PARP-7 revealed its binding features and provided insightful information for further developing highly potent and selective PARP-1 and/or PARP-7 inhibitors.


  • Organizational Affiliation

    Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1, processed C-terminus
A, B
350Homo sapiensMutation(s): 1 
Gene Names: PARP1ADPRTPPOL
EC: 2.4.2 (UniProt), 2.4.2.30 (UniProt)
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1WI
Query on 1WI

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
1-[[4-fluoranyl-3-(3-oxidanylidene-4-pentan-3-yl-piperazin-1-yl)carbonyl-phenyl]methyl]quinazoline-2,4-dione
C25 H27 F N4 O4
WKXCQZQWHUTWSY-UHFFFAOYSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.428α = 90
b = 92.007β = 90
c = 162.805γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
MOLREPphasing
PHENIXrefinement
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81673300
National Natural Science Foundation of China (NSFC)China82173693

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release