MolNFT v1 · #107798 · protein
Human ARTD1 (PARP1) - catalytic domain in complex with inhibitor talazoparib
4UND · Poly [ADP-ribose] polymerase 1: “Human ARTD1 (PARP1) - catalytic domain in complex with inhibitor talazoparib”. X-ray diffraction, 2 ligands (2YQ, NA), 6 pockets (best druggability 0.78). MolNFT v1 #107798 on GenesisL1: 3D…
- PDB
- 4UND
- Type
- protein
- Length
- 705 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
- 2YQ, NA
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 356 | 37% helix, 22% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 349 | 38% helix, 23% strand | P09874 |
Ligands and binding sites
- 2YQ · (8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2, 4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.78 | 0.85 | 50 | 2YQ |
| 2 | 485 | 0.78 | 0.85 | 44 | 2YQ |
| 3 | 411 | 0.66 | 0.79 | 43 | empty |
| 4 | 249 | 0.57 | 0.78 | 38 | empty |
| 5 | 252 | 0.51 | 0.75 | 26 | NA |
Interfaces
1 interface between chains.
- A–B · 831 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4UND · Human ARTD1 (PARP1) - catalytic domain in complex with inhibitor talazoparib · 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 4UND · PDBe 4UND · UniProt P09874
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