MolNFT v1 · #172686 · protein
Crystal structure of the catalytic domain of human PARP1 in complex with olaparib
7AAD · Poly [ADP-ribose] polymerase 1: “Crystal structure of the catalytic domain of human PARP1 in complex with olaparib”. X-ray diffraction, 2 ligands (09L, SO4), 8 pockets (best druggability 0.83). MolNFT v1 #172686 on GenesisL1: 3D…
- PDB
- 7AAD
- Type
- protein
- Length
- 700 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, 2.4.2.-
- UniProt
- P09874
- Ligands
- 09L, SO4
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 350 | 40% helix, 25% strand | P09874 |
Ligands and binding sites
- 09L · 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.83 | 0.85 | 77 | 09L, SO4 |
| 2 | 462 | 0.80 | 0.88 | 46 | 09L, SO4 |
| 3 | 103 | 0.44 | 0.78 | 17 | empty |
| 4 | 75 | 0.43 | 0.80 | 18 | empty |
| 5 | 70 | 0.39 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 812 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7AAD · Crystal structure of the catalytic domain of human PARP1 in complex with olaparib · 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 7AAD · PDBe 7AAD · UniProt P09874
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