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Structure of human PARP1 catalytic domain bound to a quinazoline-2, 4(1H,3H)-dione inhibitor

Analyse Structure of human PARP1 catalytic domain bound to a quinazoline-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KPQ
Type: protein
Length: 698 residues
Chains: 2
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: 6X2
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	349	39% helix, 25% strand	P09874

Ligands and binding sites

6X2 · 1-[[4-fluoranyl-3-[(3R)-3-methyl-4-propyl-piperazin-1-yl]carbonyl-phenyl]methyl]quinazoline-2,4-dione · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	692	0.82	0.86	73	6X2
2	409	0.81	0.89	43	6X2
3	56	0.48	0.86	13	empty
4	66	0.47	0.83	16	empty
5	56	0.41	0.82	18	empty

Interfaces

1 interface between chains.

A–B · 889 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5KPQ · Structure of human PARP1 catalytic domain bound to a quinazoline-2,4(1H,3H)-dione… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt P09874
Elsewhere: RCSB PDB 5KPQ · PDBe 5KPQ · UniProt P09874

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