MolNFT v1 · #184359 · protein
PARP1 catalytic domain in complex with isoquinolone-based inhibitor (compound 16)
7ONS · Poly [ADP-ribose] polymerase 1: “PARP1 catalytic domain in complex with isoquinolone-based inhibitor (compound 16)”. X-ray diffraction, 2 ligands (VKT, SO4), 10 pockets (best druggability 0.79). MolNFT v1 #184359 on GenesisL1: 3D…
- PDB
- 7ONS
- 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, 2.4.2.-
- UniProt
- P09874
- Ligands
- VKT, SO4
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 350 | 40% helix, 25% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 348 | 40% helix, 23% strand | P09874 |
Ligands and binding sites
- VKT · 7-[[4-(1,5-dimethylimidazol-2-yl)piperazin-1-yl]methyl]-3-ethyl-1~{H}-quinolin-2-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.79 | 0.88 | 36 | VKT |
| 2 | 393 | 0.77 | 0.87 | 41 | VKT |
| 3 | 480 | 0.71 | 0.81 | 48 | SO4 |
| 4 | 53 | 0.48 | 0.86 | 13 | empty |
| 5 | 126 | 0.47 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 829 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7ONS · PARP1 catalytic domain in complex with isoquinolone-based inhibitor (compound 16) · 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 7ONS · PDBe 7ONS · UniProt P09874
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