Research workbench
PARP1 catalytic domain in complex with a selective pyridine carboxamide-based inhibitor (compound 22)
Analyse PARP1 catalytic domain in complex with a selective pyridine carboxamide-based… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ONT
- Type
- protein
- Length
- 700 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
- VKQ, SO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 350 | 40% helix, 25% strand | P09874 |
Ligands and binding sites
- VKQ · 5-[4-[(3-ethyl-2-oxidanylidene-1~{H}-quinolin-7-yl) methyl]piperazin-1-yl]-~{N}-methyl-pyridine-2-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.81 | 0.84 | 87 | VKQ, SO4 |
| 2 | 349 | 0.78 | 0.88 | 35 | VKQ |
| 3 | 92 | 0.49 | 0.82 | 17 | empty |
| 4 | 106 | 0.43 | 0.78 | 16 | empty |
| 5 | 63 | 0.39 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 766 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7ONT · PARP1 catalytic domain in complex with a selective pyridine carboxamide-based 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 7ONT · PDBe 7ONT · UniProt P09874
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