Research workbench
Structure of human PARP1 catalytic domain bound to a quinazoline-2, 4(1H,3H)-dione inhibitor
Analyse Structure of human PARP1 catalytic domain bound to a quinazoline-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KPO
- Type
- protein
- Length
- 701 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
- 6WY
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 351 | 38% helix, 24% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 350 | 37% helix, 23% strand | P09874 |
Ligands and binding sites
- 6WY · 1-[[3-(4-ethyl-3-oxidanylidene-piperazin-1-yl)carbonyl-4-fluoranyl-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
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 | 794 | 0.82 | 0.85 | 79 | 6WY |
| 2 | 389 | 0.80 | 0.89 | 38 | 6WY |
| 3 | 63 | 0.51 | 0.86 | 14 | empty |
| 4 | 64 | 0.50 | 0.86 | 14 | empty |
| 5 | 115 | 0.44 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 857 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5KPO · 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
- P09874 · AlphaFold monomer V2.0 prediction for poly [ADP-ribose] polymerase 1 (P09874) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 5KPO · PDBe 5KPO · UniProt P09874
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