5XSR

novel orally efficacious inhibitors complexed with PARP1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report



Literature

Design and synthesis of 2-(4,5,6,7-tetrahydrothienopyridin-2-yl)-benzoimidazole carboxamides as novel orally efficacious Poly(ADP-ribose)polymerase (PARP) inhibitors

Chen, X., Huan, X., Liu, Q., Wang, Y., He, Q., Tan, C., Chen, Y., Ding, J., Xu, Y., Miao, Z., Yang, C.

(2018) Eur J Med Chem 145: 389-403

  • DOI: 10.1016/j.ejmech.2018.01.018
  • Primary Citation of Related Structures:  
    5XSR, 5XSU, 5XST

  • PubMed Abstract: 

    • The nuclear protein poly(ADP-ribose) polymerases-1/2 (PARP-1/2) are involved in DNA repair damaged by endogenous or exogenous process. And PARP-1/2 inhibitors have been proved to be clinically efficacious for DNA repair deficient tumors in the past d ...

    The nuclear protein poly(ADP-ribose) polymerases-1/2 (PARP-1/2) are involved in DNA repair damaged by endogenous or exogenous process. And PARP-1/2 inhibitors have been proved to be clinically efficacious for DNA repair deficient tumors in the past decade. We have developed a series of 4,5,6,7-tetrahydrothienopyridin-2-yl benzimidazole carboxamides as novel and potent PARP-1/2 inhibitors. The best compound resulted from this series is compound 27 which displays excellent PARP-1 and PARP-2 inhibitory activity with IC 50 of 18 nM and 42 nM, respectively. Furthermore, it can selectively kill BRCA2 deficient V-C8 cells with a CC 50 of 920 nM. In the MDA-MB-436 (BRCA-1 mutant) xenograft model, this compound was well tolerated and showed single-agent activity. Based on the results above, compound 27 has been selected as a lead candidate targeting PARP-1/2 and its preclinical characterization is also underway.

    Organizational Affiliation: 

    Synthetic Organic & Medicinal Chemistry Laboratory, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. Electronic address: chyang@simm.ac.cn.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1A355Homo sapiensMutation(s): 1 
Gene Names: PARP1, ADPRT, PPOL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
Find proteins for P09874 (Homo sapiens)
Explore P09874 
Go to UniProtKB:  P09874
NIH Common Fund Data Resources
PHAROS  P09874
GTEx  ENSG00000143799
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8EC
Query on 8EC
Download CCD File 
A
6-fluoranyl-2-(4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl)-1~{H}-benzimidazole-4-carboxamide
C15 H13 F N4 O S
DAIMOGAYMHVUBZ-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8ECIC50:  17   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.08α = 90
b = 94.08β = 90
c = 225.42γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2017-06-15 
  • Released Date: 2018-04-25 
    • Deposition Author(s): Liu, Q., Xu, Y.

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release