4ZZZ: Human PARP1 catalytic domain

Structure of human PARP1 catalytic domain bound to an isoindolinone inhibitor. Determined by X-ray diffraction at 1.9 Å resolution. Released 12 Aug 2015.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 5,676
Mol. weight: 82 kDa
Ligands: FSU
Released: 12 Aug 2015

Explore 4ZZZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ZZZ contains 41 α-helices and 40 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	667-676	10
α-helix	679-688	10
β-strand	691	1	1
α-helix	698-700	3
α-helix	703-721	19
α-helix	726-739	14
β-strand	742	1	1
α-helix	748-751	4
α-helix	755-779	25
α-helix	789-795	7
β-strand	799-803	5	2
α-helix	804-805	2
α-helix	809-820	12
β-strand	829-841	13	2
α-helix	844-848	5
α-helix	849-853	5
β-strand	857-864	8	2
α-helix	868-875	8
α-helix	879-881	3
α-helix	886-888	3
β-strand	895-897	3	3
β-strand	898	1	2
α-helix	901-905	5
α-helix	906-908	3
β-strand	911	1	4
β-strand	914	1	4
β-strand	916-925	10	2
β-strand	929-932	4	3
β-strand	936	1	5
α-helix	941-942	2
β-strand	947-950	4	3
α-helix	951	1
β-strand	952-956	5	6
β-strand	962-964	3	2
β-strand	967-969	3	2
α-helix	973	1
β-strand	974-976	3	6
β-strand	984-986	3	6
β-strand	988-991	4	3
α-helix	994-996	3
β-strand	997-1009	13	2

Chain B: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	667-676	10
α-helix	679-688	10
β-strand	691	1	7
α-helix	698-700	3
α-helix	703-722	20
α-helix	726-739	14
β-strand	742	1	7
α-helix	748-751	4
α-helix	755-779	25
α-helix	789-797	9
β-strand	799-803	5	8
α-helix	809-820	12
β-strand	829-841	13	8
α-helix	844-848	5
α-helix	850-853	4
β-strand	857-864	8	8
α-helix	866-868	3
α-helix	869-875	7
α-helix	879-881	3
α-helix	886-888	3
β-strand	895-897	3	9
β-strand	898	1	8
α-helix	901-906	6
β-strand	911	1	10
β-strand	914	1	10
β-strand	916-925	10	8
β-strand	929-932	4	9
β-strand	936	1	5
α-helix	941-942	2
β-strand	947-950	4	9
α-helix	951	1
β-strand	952-956	5	11
α-helix	958-960	3
β-strand	962-964	3	8
β-strand	967-969	3	8
β-strand	974-976	3	11
β-strand	984-986	3	11
β-strand	988-991	4	9
α-helix	994-996	3
β-strand	997-1009	13	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Poly [ADP-ribose] polymerase 1	A, B	protein	362	HOMO SAPIENS	P09874 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4ZZZ_1 POLY [ADP-RIBOSE] POLYMERASE 1 (chains A, B)
GPLTVNPGTKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSI
LSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIE
VAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLE
VIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFG
KGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLG
KTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKTS
LW

Ligands and cofactors

ID	Name	Formula	Copies
FSU	2-(3-methoxypropyl)-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide	C13 H16 N2 O3	2

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

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. et al. J Med Chem (2015) 58:6875. DOI 10.1021/ACS.JMEDCHEM.5B00680 · PubMed

Other PDB entries of the same protein (UniProt P09874 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6NRH 1.5 Å, Crystal Structure of human PARP-1 ART domain bound inhibitor UTT63
9ETQ 1.59 Å, Crystal structure of PARP1 catalytic domain bound to AZD5305 (SARUPARIB)
7AAC 1.59 Å, Crystal structure of the catalytic domain of human PARP1 in complex with veliparib
6NRJ 1.65 Å, Crystal Structure of human PARP-1 ART domain bound to inhibitor UTT93
7KK2 1.7 Å, Structure of the catalytic domain of PARP1
2RIQ 1.7 Å, Crystal Structure of the Third Zinc-binding domain of human PARP-1
6NRG 1.7 Å, Crystal Structure of human PARP-1 ART domain bound to inhibitor UTT57
7KK5 1.7 Å, Structure of the catalytic domain of PARP1 in complex with niraparib
7AAA 1.74 Å, Crystal structure of the catalytic domain of human PARP1 (apo)
6NTU 1.8 Å, Crystal Structure of human PARP-1 ART domain bound to inhibitor UKTT-15
9ETR 1.82 Å, Crystal structure of PARP1 catalytic domain bound to AZD9574
7ONT 1.85 Å, PARP1 catalytic domain in complex with a selective pyridine carboxamide-based inhibitor…

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