MolNFT v1 · #138719 · protein
Structure of human PARP1 catalytic domain bound to a benzoimidazole inhibitor
5WS1 · Poly [ADP-ribose] polymerase 1: “Structure of human PARP1 catalytic domain bound to a benzoimidazole inhibitor”. X-ray diffraction, 1 ligand (7U9), 7 pockets (best druggability 0.80). MolNFT v1 #138719 on GenesisL1: 3D structure…
- PDB
- 5WS1
- Type
- protein
- Length
- 702 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
- 7U9
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 351 | 40% helix, 24% strand | P09874 |
Ligands and binding sites
- 7U9 · 2-[(3R)-3-azanylpyrrolidin-1-yl]carbonyl-1H-benzimidazole-4-carboxamide · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.80 | 0.89 | 38 | 7U9 |
| 2 | 330 | 0.80 | 0.90 | 36 | 7U9 |
| 3 | 242 | 0.66 | 0.83 | 30 | empty |
| 4 | 83 | 0.57 | 0.87 | 16 | empty |
| 5 | 74 | 0.49 | 0.84 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 974 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5WS1 · Structure of human PARP1 catalytic domain bound to a benzoimidazole 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 5WS1 · PDBe 5WS1 · UniProt P09874
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.