Research workbench
Structure of EV71 3C in complex with rupintrivir (AG7088)
Analyse Structure of EV71 3C in complex with rupintrivir (AG7088) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SJO
- Type
- protein
- Length
- 1,432 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C protease
- EC
- 3.4.22.28
- UniProt
- E0WWC7
- Ligands
- AG7
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | 3C protease (EC 3.4.22.28) | protein | 179 | 11% helix, 55% strand | E0WWC7 |
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 · 8 copies · chains A, B, H, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.78 | 0.80 | 93 | empty |
| 2 | 441 | 0.69 | 0.80 | 62 | AG7 |
| 3 | 645 | 0.68 | 0.77 | 75 | AG7 |
| 4 | 334 | 0.67 | 0.81 | 39 | empty |
| 5 | 265 | 0.59 | 0.79 | 29 | empty |
Interfaces
12 interfaces between chains.
- A–E · 538 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 339 Ų buried · 2 hydrogen bonds · protein-protein
- D–H · 292 Ų buried · 2 hydrogen bonds · protein-protein
- C–H · 235 Ų buried · 1 hydrogen bond · protein-protein
- E–G · 229 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 3SJO · structure of EV71 3C in complex with Rupintrivir (AG7088) · 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 E0WWC7
- Elsewhere: RCSB PDB 3SJO · PDBe 3SJO · UniProt E0WWC7
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