MolNFT v1 · #15698 · protein
The structure of rhinovirus 16 when complexed with pleconaril, an antiviral compound
1NCR · Coat protein VP1: “The structure of rhinovirus 16 when complexed with pleconaril, an antiviral compound”. X-ray diffraction, 3 ligands (W11, MYR, ZN), 13 pockets (best druggability 0.77). MolNFT v1 #15698 on GenesisL1: 3D structure…
- PDB
- 1NCR
- Type
- protein
- Length
- 804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein VP1; Coat protein VP2; Coat protein VP3; Coat protein VP4
- UniProt
- Q82122
- Ligands
- W11, MYR, ZN
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coat protein VP1 | protein | 285 | 15% helix, 31% strand | Q82122 |
| B | Coat protein VP2 | protein | 252 | 13% helix, 37% strand | Q82122 |
| C | Coat protein VP3 | protein | 238 | 9% helix, 31% strand | Q82122 |
| D | Coat protein VP4 | protein | 29 | 10% helix, 21% strand | Q82122 |
Ligands and binding sites
- W11 · 3-{3,5-dimethyl-4-[3-(3-methyl-isoxazol-5-yl)-propoxy]-phenyl}-5-trifluoromethyl-[1,2,4]oxadiazole · ligand · chains A, C
- MYR · Myristic acid · ligand · chains D
- ZN · Zinc ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.77 | 0.86 | 66 | W11 |
| 2 | 327 | 0.54 | 0.75 | 45 | empty |
| 3 | 193 | 0.50 | 0.77 | 23 | empty |
| 4 | 105 | 0.47 | 0.80 | 23 | empty |
| 5 | 153 | 0.44 | 0.75 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4280 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 2090 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 1686 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 683 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 372 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1NCR · The structure of Rhinovirus 16 when complexed with pleconaril, an antiviral compound · 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 Q82122
- Elsewhere: RCSB PDB 1NCR · PDBe 1NCR · UniProt Q82122
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