Research workbench
Structure of the catalytic domain of PARP1 in complex with niraparib
Analyse Structure of the catalytic domain of PARP1 in complex with niraparib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KK5
- Type
- protein
- Length
- 1,358 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, 2.4.2.-
- UniProt
- P09874
- Ligands
- 3JD, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 339 | 39% helix, 25% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 343 | 40% helix, 25% strand | P09874 |
| C | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 344 | 39% helix, 24% strand | P09874 |
| D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 332 | 38% helix, 25% strand | P09874 |
Ligands and binding sites
- 3JD · 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 19 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.77 | 0.84 | 45 | 3JD, SO4 |
| 2 | 524 | 0.76 | 0.84 | 44 | 3JD, SO4 |
| 3 | 512 | 0.76 | 0.84 | 43 | 3JD, SO4 |
| 4 | 495 | 0.76 | 0.84 | 39 | 3JD, SO4 |
| 5 | 441 | 0.68 | 0.80 | 54 | empty |
Interfaces
5 interfaces between chains.
- A–C · 794 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 765 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 521 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 448 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 348 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7KK5 · Structure of the catalytic domain of PARP1 in complex with niraparib · 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 7KK5 · PDBe 7KK5 · UniProt P09874
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