Research workbench
Complex structure of hevb EV93 main protease 3C with rupintrivir (AG7088)
Analyse Complex structure of hevb EV93 main protease 3C 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
- 3RUO
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hevb EV93 3C protease
- EC
- 3.4.22.28
- UniProt
- Q5DSM6
- Ligands
- AG7, MG, CL
- Pockets
- 3 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hevb EV93 3C protease (EC 3.4.22.28) | protein | 184 | 13% helix, 56% strand | Q5DSM6 |
| B | Hevb EV93 3C protease (EC 3.4.22.28) | protein | 181 | 13% helix, 56% strand | Q5DSM6 |
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
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.32 | 0.74 | 23 | empty |
| 2 | 56 | 0.31 | 0.75 | 16 | empty |
| 3 | 84 | 0.30 | 0.72 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 751 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3RUO · Complex structure of HevB EV93 main protease 3C 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 Q5DSM6
- Elsewhere: RCSB PDB 3RUO · PDBe 3RUO · UniProt Q5DSM6
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