MolNFT v1 · #18248 · protein
Binding of the antiviral drug WIN51711 to the sabin strain of type 3 poliovirus: structural comparison with drug binding in rhinovirus 14
1PIV · Poliovirus type 3 (subunit VP1): “Binding of the antiviral drug WIN51711 to the sabin strain of type 3 poliovirus: structural comparison with…”. X-ray diffraction, 2 ligands (MYR, W71), 14 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 1PIV
- Type
- protein
- Length
- 846 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poliovirus type 3 (subunit VP1); Poliovirus type 3 (subunit VP2); Poliovirus type 3…
- UniProt
- P03302
- Ligands
- MYR, W71
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | Poliovirus type 3 (subunit VP1) | protein | 4 | 0% helix, 50% strand | — |
| 1 | Poliovirus type 3 (subunit VP1) | protein | 279 | 9% helix, 32% strand | P03302 |
| 2 | Poliovirus type 3 (subunit VP2) | protein | 266 | 13% helix, 38% strand | P03302 |
| 3 | Poliovirus type 3 (subunit VP3) | protein | 235 | 9% helix, 30% strand | P03302 |
| 4 | Poliovirus type 3 (subunit VP4) | protein | 62 | 11% helix, 15% strand | P03302 |
Ligands and binding sites
- MYR · Myristic acid · ligand · chains 4
- W71 · 5-(7-(4-(4,5-dihydro-2-oxazolyl)phenoxy)heptyl)-3-methyl isoxazole · ligand · chains 1, 3
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.80 | 0.84 | 92 | W71 |
| 2 | 73 | 0.68 | 0.94 | 22 | empty |
| 3 | 281 | 0.51 | 0.75 | 51 | empty |
| 4 | 161 | 0.47 | 0.76 | 32 | empty |
| 5 | 76 | 0.42 | 0.80 | 13 | empty |
Interfaces
7 interfaces between chains.
- 1–3 · 3969 Ų buried · 75 hydrogen bonds · protein-protein
- 1–2 · 2371 Ų buried · 41 hydrogen bonds · protein-protein
- 2–3 · 1712 Ų buried · 17 hydrogen bonds · protein-protein
- 1–4 · 908 Ų buried · 12 hydrogen bonds · protein-protein
- 3–4 · 892 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (myristoylation).
Compared structures
- 1PIV · Binding of the antiviral drug WIN51711 to the sabin strain of type 3 poliovirus… · the same entry in another collection · chain 0 against 0, 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 P03302
- Elsewhere: RCSB PDB 1PIV · PDBe 1PIV · UniProt P03302
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