6I8M

THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH ISOINDOLINONE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of Stereospecific PARP-1 Inhibitor Isoindolinone NMS-P515.

Papeo, G.Orsini, P.Avanzi, N.R.Borghi, D.Casale, E.Ciomei, M.Cirla, A.Desperati, V.Donati, D.Felder, E.R.Galvani, A.Guanci, M.Isacchi, A.Posteri, H.Rainoldi, S.Riccardi-Sirtori, F.Scolaro, A.Montagnoli, A.

(2019) ACS Med Chem Lett 10: 534-538

  • DOI: 10.1021/acsmedchemlett.8b00569
  • Primary Citation of Related Structures:  
    6I8M, 6I8T

  • PubMed Abstract: 
  • Poly(ADP-ribose) polymerase-1 (PARP-1) is an enzyme involved in signaling and repair of DNA single strand breaks. PARP-1 employs NAD + to modify substrate proteins via the attachment of poly(ADP-ribose) chains. PARP-1 is a well established target in oncology, as testified by the number of marketed drugs (e ...

    Poly(ADP-ribose) polymerase-1 (PARP-1) is an enzyme involved in signaling and repair of DNA single strand breaks. PARP-1 employs NAD + to modify substrate proteins via the attachment of poly(ADP-ribose) chains. PARP-1 is a well established target in oncology, as testified by the number of marketed drugs (e.g., Lynparza, Rubraca, Zejula, and Talzenna) used for the treatment of ovarian, breast, and prostate tumors. Efforts in investigating an uncharted region of the previously identified isoindolinone carboxamide series delivered ( S )- 13 (NMS-P515), a potent inhibitor of PARP-1 both in biochemical ( K d : 0.016 μM) and cellular (IC 50 : 0.027 μM) assays. Cocrystal structure allowed explaining NMS-P515 stereospecific inhibition of the target. After having ruled out potential loss of enantiopurity in vitro and in vivo, NMS-P515 was synthesized in an asymmetric fashion. NMS-P515 ADME profile and its antitumor activity in a mouse xenograft cancer model render the compound eligible for further optimization.


    Organizational Affiliation

    Oncology, Nerviano Medical Sciences S.r.l., Viale Pasteur 10, 20014 Nerviano, Milan, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1A363Gallus gallusMutation(s): 0 
Gene Names: PARP1ADPRT
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt
Find proteins for P26446 (Gallus gallus)
Explore P26446 
Go to UniProtKB:  P26446
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H7W (Subject of Investigation/LOI)
Query on H7W

Download Ideal Coordinates CCD File 
B [auth A](1~{S})-2-(1-cyclohexylpiperidin-4-yl)-1-methyl-3-oxidanylidene-1~{H}-isoindole-4-carboxamide
C21 H29 N3 O2
OYGLTKXMFGWXJT-AWEZNQCLSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
H7W BindingDB:  6I8M Kd: min: 10, max: 30 (nM) from 3 assay(s)
IC50: min: 27, max: 50 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.053α = 90
b = 64.299β = 90
c = 97.707γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release