Research workbench
Structure of human PARP1 catalytic domain bound to an isoindolinone inhibitor
Analyse Structure of human PARP1 catalytic domain bound to an isoindolinone inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZZZ
- Type
- protein
- Length
- 692 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
- FSU, SO4
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 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) | protein | 350 | 38% helix, 25% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 342 | 40% helix, 25% strand | P09874 |
Ligands and binding sites
- FSU · 2-(3-methoxypropyl)-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 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 | 715 | 0.81 | 0.85 | 63 | GOL, FSU |
| 2 | 454 | 0.79 | 0.87 | 45 | SO4, GOL, FSU |
| 3 | 67 | 0.56 | 0.88 | 15 | empty |
| 4 | 141 | 0.50 | 0.79 | 18 | empty |
| 5 | 160 | 0.48 | 0.77 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 900 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4ZZZ · Structure of human PARP1 catalytic domain bound to an isoindoli inhibitor · 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 4ZZZ · PDBe 4ZZZ · UniProt P09874
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