Research workbench
Structure of the SARS-cov-2 main protease in complex with inhibitor MPI20
Analyse Structure of the SARS-cov-2 main protease in complex with inhibitor MPI20 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RVT
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- UniProt
- P0DTD1
- Ligands
- 7XK
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase | protein | 300 | 25% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- 7XK · N~2~-[(2S)-2-{[(benzyloxy)carbonyl]amino}-2-cyclopropylacetyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-methyl-L-leucinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.77 | 0.79 | 85 | empty |
| 2 | 418 | 0.57 | 0.74 | 52 | empty |
| 3 | 96 | 0.42 | 0.78 | 15 | empty |
| 4 | 126 | 0.41 | 0.75 | 25 | empty |
| 5 | 135 | 0.39 | 0.74 | 28 | 7XK |
Interfaces
1 interface between chains.
- A–B · 1674 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7RVT · Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI20 · 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 7RVT · PDBe 7RVT · UniProt P0DTD1
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