MolNFT v1 · #15710 · protein
The structure of HRV16, when complexed with pleconaril, an antiviral compound
1ND3 · Coat protein VP1: “The structure of HRV16, when complexed with pleconaril, an antiviral compound”. X-ray diffraction, 2 ligands (W11, ZN), 12 pockets (best druggability 0.81). MolNFT v1 #15710 on GenesisL1: 3D structure, binding…
- PDB
- 1ND3
- 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, ZN
- Pockets
- 12 · best druggability 0.81
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 | 16% helix, 32% 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, 14% 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
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.81 | 0.93 | 37 | W11 |
| 2 | 216 | 0.56 | 0.78 | 27 | empty |
| 3 | 295 | 0.53 | 0.75 | 40 | empty |
| 4 | 110 | 0.48 | 0.80 | 21 | empty |
| 5 | 159 | 0.45 | 0.75 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4259 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 2110 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 1686 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 721 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 357 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1ND3 · The structure of HRV16, 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 1ND3 · PDBe 1ND3 · UniProt Q82122
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