MolNFT v1 · #87862 · protein
Crystal structure of human enterovirus 71 in complex with the uncoating inhibitor GPP2
4CDQ · VP1: “Crystal structure of human enterovirus 71 in complex with the uncoating inhibitor GPP2”. X-ray diffraction, 2 ligands (7VR, NA), 14 pockets (best druggability 0.80). MolNFT v1 #87862 on GenesisL1: 3D structure, binding sites…
- PDB
- 4CDQ
- Type
- protein
- Length
- 842 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- B2ZUN0
- Ligands
- 7VR, NA
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 297 | 14% helix, 27% strand | B2ZUN0 |
| B | VP2 | protein | 245 | 14% helix, 38% strand | B2ZUN0 |
| C | VP3 | protein | 242 | 13% helix, 30% strand | B2ZUN0 |
| D | VP4 | protein | 58 | 12% helix, 12% strand | B2ZUN0 |
Ligands and binding sites
- 7VR · 4-((5-(2-oxo-3-(pyridin-4-yl)imidazolidin-1-yl)pentyl)oxy)benzaldehyde O-ethyl oxime · ligand · chains A, C
- NA · Sodium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.80 | 0.88 | 56 | 7VR |
| 2 | 243 | 0.60 | 0.80 | 37 | empty |
| 3 | 54 | 0.59 | 0.91 | 20 | empty |
| 4 | 185 | 0.48 | 0.76 | 29 | empty |
| 5 | 122 | 0.48 | 0.79 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4054 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 2693 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 1689 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1517 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1160 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4CDQ · Crystal structure of human Enterovirus 71 in complex with the uncoating inhibitor GPP2 · 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 B2ZUN0
- Elsewhere: RCSB PDB 4CDQ · PDBe 4CDQ · UniProt B2ZUN0
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