MolNFT v1 · #124794 · protein
Structure of human PARP1 catalytic domain bound to a quinazoline-2, 4(1H,3H)-dione inhibitor
5KPP · Poly [ADP-ribose] polymerase 1: “Structure of human PARP1 catalytic domain bound to a quinazoline-2, 4(1H,3H)-dione inhibitor”. X-ray diffraction, 1 ligand (6WZ), 8 pockets (best druggability 0.80). MolNFT v1 #124794 on GenesisL1…
- PDB
- 5KPP
- Type
- protein
- Length
- 698 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
- 6WZ
- Pockets
- 8 · best druggability 0.80
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) | protein | 349 | 40% helix, 25% strand | P09874 |
Ligands and binding sites
- 6WZ · 1-[[4-fluoranyl-3-[(3R)-3-methyl-4-[2,2,2-tris(fluoranyl)ethyl]piperazin-1-yl]carbonyl-phenyl]methyl]quinazoline-2,4-dione · ligand · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.80 | 0.89 | 37 | 6WZ |
| 2 | 395 | 0.80 | 0.89 | 36 | 6WZ |
| 3 | 259 | 0.67 | 0.84 | 37 | empty |
| 4 | 91 | 0.54 | 0.85 | 16 | empty |
| 5 | 51 | 0.47 | 0.86 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 865 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5KPP · Structure of human PARP1 catalytic domain bound to a quinazoline-2,4(1H,3H)-dione… · 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 5KPP · PDBe 5KPP · UniProt P09874
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