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
- 5WRY
- Type
- protein
- Length
- 703 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
- 4YR
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 351 | 39% helix, 25% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 352 | 39% helix, 23% strand | P09874 |
Ligands and binding sites
- 4YR · N-[(3R)-1-(cyclopropylmethyl)pyrrolidin-3-yl]-5-[(2,4-dioxo-3,4-dihydroquinazolin-1(2H)-yl)methyl]-2-fluorobenzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.82 | 0.86 | 74 | 4YR |
| 2 | 455 | 0.80 | 0.88 | 46 | 4YR |
| 3 | 181 | 0.53 | 0.79 | 28 | empty |
| 4 | 64 | 0.49 | 0.85 | 14 | empty |
| 5 | 77 | 0.47 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 973 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5WRY · 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 5WRY · PDBe 5WRY · UniProt P09874
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.