MolNFT v1 · #49821 · protein
Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses
2R04 · Human rhinovirus 14 coat protein (subunit VP1): “Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses”. X-ray diffraction, 1 ligand (W71), 11 pockets (best druggability 0.82). MolNFT v1 #49821…
- PDB
- 2R04
- Type
- protein
- Length
- 804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human rhinovirus 14 coat protein (subunit VP1); Human rhinovirus 14 coat protein (subunit…
- UniProt
- P03303
- Ligands
- W71
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Human rhinovirus 14 coat protein (subunit VP1) | protein | 273 | 11% helix, 33% strand | P03303 |
| 2 | Human rhinovirus 14 coat protein (subunit VP2) | protein | 255 | 15% helix, 37% strand | P03303 |
| 3 | Human rhinovirus 14 coat protein (subunit VP3) | protein | 236 | 9% helix, 32% strand | P03303 |
| 4 | Human rhinovirus 14 coat protein (subunit VP4) | protein | 40 | 18% helix, 3% strand | P03303 |
Ligands and binding sites
- 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
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.82 | 0.92 | 54 | W71 |
| 2 | 199 | 0.53 | 0.78 | 35 | empty |
| 3 | 168 | 0.46 | 0.76 | 34 | empty |
| 4 | 103 | 0.45 | 0.79 | 22 | empty |
| 5 | 110 | 0.40 | 0.76 | 21 | empty |
Interfaces
6 interfaces between chains.
- 1–3 · 4138 Ų buried · 70 hydrogen bonds · protein-protein
- 1–2 · 2110 Ų buried · 44 hydrogen bonds · protein-protein
- 2–3 · 1705 Ų buried · 15 hydrogen bonds · protein-protein
- 1–4 · 956 Ų buried · 14 hydrogen bonds · protein-protein
- 3–4 · 898 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2R04 · Structural analysis of antiviral agents that interact with the capsid of human… · the same entry in another collection · chain 3 against 3, 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 P03303
- Elsewhere: RCSB PDB 2R04 · PDBe 2R04 · UniProt P03303
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