Research workbench
The structure of rhinovirus 16 when complexed with pleconaril, an antiviral compound
Analyse The structure of rhinovirus 16 when complexed with pleconaril, an antiviral… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.