Research workbench
Structure of human PARP1 catalytic domain bound to a phthalazinone inhibitor
Analyse Structure of human PARP1 catalytic domain bound to a phthalazinone inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WRZ
- 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
- 7U3
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 351 | 39% helix, 24% strand | P09874 |
Ligands and binding sites
- 7U3 · 7-fluoranyl-4-[[(3R)-pyrrolidin-3-yl]methoxy]-2H-phthalazin-1-one · ligand · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.80 | 0.90 | 37 | 7U3 |
| 2 | 349 | 0.80 | 0.90 | 39 | 7U3 |
| 3 | 447 | 0.70 | 0.81 | 50 | empty |
| 4 | 85 | 0.55 | 0.86 | 15 | empty |
| 5 | 102 | 0.47 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 926 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5WRZ · Structure of human PARP1 catalytic domain bound to a phthalazi 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 5WRZ · PDBe 5WRZ · UniProt P09874
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