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Structure of human PARP1 catalytic domain bound to an isoindolinone inhibitor

Analyse Structure of human PARP1 catalytic domain bound to an isoindolinone inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5A00
Type: protein
Length: 340 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Poly [ADP-ribose] polymerase 1
EC: 2.4.2.30
UniProt: P09874
Ligands: D7N, SO4
Pockets: 2 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	340	39% helix, 23% strand	P09874

Ligands and binding sites

D7N · 2-[1-(4,4-Difluorocyclohexyl)-piperidin-4-yl]-6-fluoro-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide · ligand · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	609	0.76	0.83	42	D7N
2	117	0.48	0.80	18	empty

Compared structures

5A00 · Structure of human PARP1 catalytic domain bound to an isoindoli inhibitor · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P09874
Elsewhere: RCSB PDB 5A00 · PDBe 5A00 · UniProt P09874

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