Research workbench
Structure of the catalytic domain of PARP1 in complex with veliparib
Analyse Structure of the catalytic domain of PARP1 in complex with veliparib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KK6
- 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
- 78P, SO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% 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 | 351 | 39% helix, 25% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 349 | 39% helix, 23% strand | P09874 |
Ligands and binding sites
- 78P · (2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium · 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.78 | 0.88 | 38 | 78P, SO4 |
| 2 | 323 | 0.78 | 0.89 | 34 | 78P, SO4 |
| 3 | 345 | 0.71 | 0.84 | 40 | empty |
| 4 | 67 | 0.45 | 0.82 | 13 | empty |
| 5 | 60 | 0.43 | 0.82 | 12 | SO4 |
Interfaces
1 interface between chains.
- A–B · 878 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7KK6 · Structure of the catalytic domain of PARP1 in complex with veliparib · 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 7KK6 · PDBe 7KK6 · UniProt P09874
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