MolNFT v1 · #93942 · protein

Crystal structure of parp catalytic domain in complex with novel inhibitors

4HHY · Poly [ADP-ribose] polymerase 1: “Crystal structure of parp catalytic domain in complex with novel inhibitors”. X-ray diffraction, 2 ligands (15R, SO4), 16 pockets (best druggability 0.81). MolNFT v1 #93942 on GenesisL1: 3D…

PDB: 4HHY
Type: protein
Length: 1,343 residues
Chains: 4
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: 15R, SO4
Pockets: 16 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	349	36% helix, 25% strand	P09874
B	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	340	39% helix, 24% strand	P09874
C	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	345	38% helix, 22% strand	P09874
D	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	309	33% helix, 19% strand	P09874

Ligands and binding sites

15R · (9aR)-1-[(1-{2-fluoro-5-[(4-oxo-3,4-dihydrophthalazin-1-yl)methyl]benzoyl}piperidin-4-yl)carbonyl]-1,2,3,8,9,9a-hexahydro-7H-benzo[de][1,7]naphthyridin-7-one · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	620	0.81	0.86	50	15R
2	981	0.79	0.81	88	15R, SO4, PEG
3	764	0.79	0.83	70	15R
4	541	0.78	0.84	46	15R
5	1123	0.74	0.77	105	empty

Interfaces

5 interfaces between chains.

A–B · 936 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 404 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 298 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 230 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 48 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4HHY · Crystal structure of PARP catalytic domain in complex with novel inhibitors · 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 4HHY · PDBe 4HHY · UniProt P09874

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