MolNFT v1 · #76956 · protein
Human enterovirus 71 3C protease mutant H133G in complex with rupintrivir
3R0F · 3C protein: “Human enterovirus 71 3C protease mutant H133G in complex with rupintrivir”. X-ray diffraction, 1 ligand (AG7), 4 pockets (best druggability 0.42). MolNFT v1 #76956 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3R0F
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C protein
- UniProt
- E7E815
- Ligands
- AG7
- Pockets
- 4 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C protein | protein | 181 | 13% helix, 54% strand | E7E815 |
| B | 3C protein | protein | 176 | 11% helix, 56% strand | E7E815 |
Ligands and binding sites
- AG7 · 4-{2-(4-fluoro-benzyl)-6-methyl-5-[(5-methyl-isoxazole-3-carbonyl)-amino]-4-oxo-heptanoylamino}-5-(2-oxo-pyrrolidin-3-yl)-pentanoic acid ethyl ester · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.42 | 0.75 | 26 | empty |
| 2 | 71 | 0.39 | 0.78 | 15 | empty |
| 3 | 69 | 0.31 | 0.74 | 16 | empty |
| 4 | 62 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 516 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3R0F · Human enterovirus 71 3C protease mutant H133G in complex with rupintrivir · 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 E7E815
- Elsewhere: RCSB PDB 3R0F · PDBe 3R0F · UniProt E7E815
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