4ZZZ | pdb_00004zzz

Structure of human PARP1 catalytic domain bound to an isoindolinone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4ZZZ/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: 1.90 Å
• R-Value Free: 
  0.265 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.228 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 82 kDa 
• Atom Count: 5,676 
• Modeled Residue Count: 692 
• Deposited Residue Count: 724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLY [ADP-RIBOSE] POLYMERASE 1	A, B	362	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 P09874 (Homo sapiens) Explore P09874  Go to UniProtKB:  P09874
PHAROS:  P09874 GTEx:  ENSG00000143799

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FSU	G [auth A], K [auth B]	2-(3-methoxypropyl)-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide C13 H16 N2 O3 VARCSQSOWLMGTH-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], H [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FSU	BindingDB:  4ZZZ	Kd: 87 (nM) from 1 assay(s)
		IC50: 5300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.265 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.228 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.9	α = 90
b = 54.05	β = 113.79
c = 92.76	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other