Research workbench
Structure of the SARS-cov-2 main protease in complex with inhibitor MPI29
Analyse Structure of the SARS-cov-2 main protease in complex with inhibitor MPI29 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S6W
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- 8G9
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 25% helix, 28% strand | P0DTD1 |
Ligands and binding sites
- 8G9 · (1R,2S,5S)-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.77 | 0.79 | 87 | empty |
| 2 | 224 | 0.53 | 0.77 | 31 | 8G9 |
| 3 | 204 | 0.50 | 0.76 | 26 | 8G9 |
| 4 | 259 | 0.47 | 0.73 | 41 | empty |
| 5 | 174 | 0.45 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1729 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent (oxidation, covalent ligand).
Compared structures
- 7S6W · Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI29 · 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 P0DTD1
- Elsewhere: RCSB PDB 7S6W · PDBe 7S6W · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.