MolNFT v1 · #120750 · protein
Crystal structure-based design and disovery of a novel PARP1 antiagonist (bl-PA10) that induces apoptosis and inhibits metastasis in triple negative breast cancer
5HA9 · Poly [ADP-ribose] polymerase 1: “Crystal structure-based design and disovery of a novel PARP1 antiagonist (bl-PA10) that induces apoptosis and…”. X-ray diffraction, 2 ligands (TP0, SO4), 9 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5HA9
- Type
- protein
- Length
- 702 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
- TP0, SO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 351 | 36% helix, 22% strand | P09874 |
Ligands and binding sites
- TP0 · Amitriptyline · ligand · chains B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.80 | 0.89 | 36 | GOL, TP0 |
| 2 | 358 | 0.79 | 0.89 | 42 | GOL, SO4 |
| 3 | 294 | 0.73 | 0.86 | 32 | empty |
| 4 | 93 | 0.50 | 0.83 | 18 | empty |
| 5 | 138 | 0.47 | 0.78 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 973 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5HA9 · Crystal structure-based design and disovery of a novel PARP1 antiagonist (BL-PA10) that… · 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 5HA9 · PDBe 5HA9 · UniProt P09874
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