Research workbench
Human ARTD1 (PARP1) - catalytic domain in complex with inhibitor niraparib
Analyse Human ARTD1 (PARP1) - catalytic domain in complex with inhibitor niraparib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R6E
- Type
- protein
- Length
- 1,398 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
- UniProt
- P09874
- Ligands
- 3JD, SO4
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 350 | 39% helix, 24% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 350 | 39% helix, 24% strand | P09874 |
| D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 348 | 39% helix, 24% 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 · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.78 | 0.85 | 41 | 3JD, GOL |
| 2 | 538 | 0.78 | 0.85 | 43 | 3JD |
| 3 | 564 | 0.78 | 0.84 | 50 | 3JD, SO4, GOL |
| 4 | 525 | 0.78 | 0.85 | 39 | 3JD, GOL |
| 5 | 1196 | 0.77 | 0.79 | 127 | empty |
Interfaces
5 interfaces between chains.
- A–C · 939 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 548 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 503 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 265 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4R6E · Human artd1 (parp1) - catalytic domain in complex with inhibitor 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 4R6E · PDBe 4R6E · UniProt P09874
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.