4ZZY | pdb_00004zzy

Structure of human PARP2 catalytic domain bound to an isoindolinone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4ZZY/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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.280 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.216 (Depositor) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1021/acs.jmedchem.5b00680
• Primary Citation Related Structures: 
  4ZZX, 4ZZY, 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.

---

Organizational Affiliation: 
• Oncology, Nerviano Medical Sciences Srl , Viale Pasteur 10, 20014 Nerviano, Milan, Italy.
Chemical Diversity Research Institute , Rabochaya St. 2 Khimki, Moscow Region 114401, Russia.
Accelera Srl , Viale Pasteur 10, 20014 Nerviano, Milan, Italy.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.5 kDa 
• Atom Count: 2,904 
• Modeled Residue Count: 351 
• Deposited Residue Count: 363 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLY [ADP-RIBOSE] POLYMERASE 2	A	363	Homo sapiens	Mutation(s): 0  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
D7N	B [auth A]	2-[1-(4,4-Difluorocyclohexyl)-piperidin-4-yl]-6-fluoro-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide C20 H24 F3 N3 O2 ARYVAQSYRLZVQD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D7N	BindingDB:  4ZZY	Kd: min: 1389, max: 1400 (nM) from 2 assay(s)
		IC50: min: 1389, max: 6600 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.280 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.216 (Depositor) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.377	α = 90
b = 74.377	β = 90
c = 148.463	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description