MolNFT v1 · #39516 · protein
A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A
2HWD · Human rhinovirus 1A coat protein (subunit VP1): “A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A”. X-ray diffraction, 1 ligand (W91), 11 pockets (best druggability 0.80). MolNFT v1 #39516 on GenesisL1: 3D…
- PDB
- 2HWD
- Type
- protein
- Length
- 793 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human rhinovirus 1A coat protein (subunit VP1); Human rhinovirus 1A coat protein (subunit…
- UniProt
- P23008
- Ligands
- W91
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Human rhinovirus 1A coat protein (subunit VP1) | protein | 283 | 9% helix, 26% strand | P23008 |
| 2 | Human rhinovirus 1A coat protein (subunit VP2) | protein | 253 | 6% helix, 32% strand | P23008 |
| 3 | Human rhinovirus 1A coat protein (subunit VP3) | protein | 238 | 8% helix, 32% strand | P23008 |
| 4 | Human rhinovirus 1A coat protein (subunit VP4) | protein | 19 | 0% helix, 0% strand | P23008 |
Ligands and binding sites
- W91 · 5-(3-(2,6-dichloro-4-(4,5-dihydro-2-oxazolyl)phenoxy)propyl)-3-methyl isoxazole · ligand · chains 1
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.80 | 0.87 | 63 | W91 |
| 2 | 324 | 0.54 | 0.74 | 40 | empty |
| 3 | 240 | 0.54 | 0.77 | 28 | empty |
| 4 | 132 | 0.46 | 0.77 | 23 | empty |
| 5 | 91 | 0.39 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- 1–3 · 4039 Ų buried · 64 hydrogen bonds · protein-protein
- 1–2 · 2221 Ų buried · 35 hydrogen bonds · protein-protein
- 2–3 · 1645 Ų buried · 18 hydrogen bonds · protein-protein
- 1–4 · 504 Ų buried · 9 hydrogen bonds · protein-protein
- 3–4 · 405 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2HWD · A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A · the same entry in another collection · chain 2 against 2, 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 P23008
- Elsewhere: RCSB PDB 2HWD · PDBe 2HWD · UniProt P23008
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