Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.70 kDa 
• Atom Count: 5927 
• Modelled Residue Count: 700 
• Deposited Residue Count: 726 
• Unique protein chains: 1

4ZZX

Structure of PARP2 catalytic domain bound to an isoindolinone inhibitor

• DOI: 10.2210/pdb4ZZX/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-04-15 Released: 2015-08-12 
• Deposition Author(s): Casale, E., Fasolini, M., Papeo, G., Posteri, H., Borghi, D., Busel, A.A., Caprera, F., Ciomei, M., Cirla, A., Corti, E., DAnello, M., Fasolini, M., Felder, E.R., Forte, B., Galvani, A., Isacchi, A., Khvat, A., Krasavin, M.Y., Lupi, R., Orsini, P., Perego, R., Pesenti, E., Pezzetta, D., Rainoldi, S., RiccardiSirtori, F., Scolaro, A., Sola, F., Zuccotto, F., Donati, D., Montagnoli, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.244 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 

Literature

Discovery of 2-[1-(4,4-Difluorocyclohexyl)Piperidin-4-Yl]-6-Fluoro-3-Oxo-2,3-Dihydro-1H-Isoindole-4-Carboxamide (Nms-P118): A Potent, Orally Available and Highly Selective Parp- 1 Inhibitor for Cancer Therapy.

Papeo, G.M.E., Posteri, H., Borghi, D., Busel, A.A., Caprera, F., Casale, E., Ciomei, M., Cirla, A., Corti, E., D'Anello, M., Fasolini, M., Forte, B., Galvani, A., Isacchi, A., Khvat, A., Krasavin, M.Y., Lupi, R., Orsini, P., Perego, R., Pesenti, E., Pezzetta, D., Rainoldi, S., Riccardi-Sirtori, F., Scolaro, A., Sola, F., Zuccotto, F., Felder, E.R., Donati, D., Montagnoli, A.

(2015) J Med Chem 58: 6875

• PubMed: 26222319 
• DOI: 10.1021/acs.jmedchem.5b00680
• Primary Citation of Related Structures:  
  4ZZY, 4ZZX, 4ZZZ, 5A00


• PubMed Abstract: 
  

The nuclear protein poly(ADP-ribose) polymerase-1 (PARP-1) has a well-established role in the signaling and repair of DNA and is a prominent target in oncology, as testified by the number of candidates in clinical testing that unselectively target both PARP-1 and its closest isoform PARP-2. The goal of our program was to find a PARP-1 selective inhibitor that would potentially mitigate toxicities arising from cross-inhibition of PARP-2. Thus, an HTS campaign on the proprietary Nerviano Medical Sciences (NMS) chemical collection, followed by SAR optimization, allowed us to discover 2-[1-(4,4-difluorocyclohexyl)piperidin-4-yl]-6-fluoro-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide (NMS-P118, 20by). NMS-P118 proved to be a potent, orally available, and highly selective PARP-1 inhibitor endowed with excellent ADME and pharmacokinetic profiles and high efficacy in vivo both as a single agent and in combination with Temozolomide in MDA-MB-436 and Capan-1 xenograft models, respectively. Cocrystal structures of 20by with both PARP-1 and PARP-2 catalytic domain proteins allowed rationalization of the observed selectivity.

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Organizational Affiliation: 

Oncology, Nerviano Medical Sciences Srl , Viale Pasteur 10, 20014 Nerviano, Milan, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLY [ADP-RIBOSE] POLYMERASE 2	A, B	363	Homo sapiens	Mutation(s): 0  Gene Names: PARP2, ADPRT2, ADPRTL2 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGN5 (Homo sapiens) Explore Q9UGN5  Go to UniProtKB:  Q9UGN5
PHAROS:  Q9UGN5 GTEx:  ENSG00000129484

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FSU	C [auth A], D [auth B]	2-(3-methoxypropyl)-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide C13 H16 N2 O3 VARCSQSOWLMGTH-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
FSU	Kd:  125   nM  BindingDB
FSU	Kd:  125   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.244 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.46	α = 90
b = 72.74	β = 90
c = 141.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-04-15 
• Released Date: 2015-08-12 
Deposition Author(s): Casale, E., Fasolini, M., Papeo, G., Posteri, H., Borghi, D., Busel, A.A., Caprera, F., Ciomei, M., Cirla, A., Corti, E., DAnello, M., Fasolini, M., Felder, E.R., Forte, B., Galvani, A., Isacchi, A., Khvat, A., Krasavin, M.Y., Lupi, R., Orsini, P., Perego, R., Pesenti, E., Pezzetta, D., Rainoldi, S., RiccardiSirtori, F., Scolaro, A., Sola, F., Zuccotto, F., Donati, D., Montagnoli, A.

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2015-09-23
  Changes: Database references
• Version 1.2: 2019-03-06
  Changes: Data collection, Experimental preparation, Other