MolNFT v1 · #87865 · protein
Crystal structure of human enterovirus 71 in complex with the uncoating inhibitor GPP3
4CDU · VP1: “Crystal structure of human enterovirus 71 in complex with the uncoating inhibitor GPP3”. X-ray diffraction, 3 ligands (YM2, NA, CL), 14 pockets (best druggability 0.80). MolNFT v1 #87865 on GenesisL1: 3D structure, binding…
- PDB
- 4CDU
- 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
- YM2, NA, CL
- 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
- YM2 · 1-[(3S)-5-[4-[(E)-ethoxyiminomethyl]phenoxy]-3-methyl-pentyl]-3-pyridin-4-yl-imidazolidin-2-one · ligand · chains A, C
- NA · Sodium ion · metal · 2 copies · chains C, D
- CL · Chloride ion · ion · chains B
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 | 406 | 0.80 | 0.88 | 53 | YM2 |
| 2 | 259 | 0.60 | 0.80 | 40 | empty |
| 3 | 54 | 0.57 | 0.90 | 20 | empty |
| 4 | 70 | 0.50 | 0.85 | 19 | empty |
| 5 | 124 | 0.47 | 0.78 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4058 Ų buried · 63 hydrogen bonds · protein-protein
- A–B · 2649 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 1705 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1512 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1153 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4CDU · Crystal structure of human Enterovirus 71 in complex with the uncoating inhibitor GPP3 · 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 4CDU · PDBe 4CDU · UniProt B2ZUN0
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