MolNFT v1 · #186943 · protein
Structure of the SARS-cov-2 main protease in complex with inhibitor MPI13
7RVO · 3C-like proteinase: “Structure of the SARS-cov-2 main protease in complex with inhibitor MPI13”. X-ray diffraction, 1 ligand (7VI), 7 pockets (best druggability 0.76). MolNFT v1 #186943 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7RVO
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- UniProt
- P0DTD1
- Ligands
- 7VI
- Pockets
- 7 · best druggability 0.76
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 | 306 | 25% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- 7VI · N-[(benzyloxy)carbonyl]-L-valyl-3-cyclopropyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alaninamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.76 | 0.79 | 81 | empty |
| 2 | 432 | 0.62 | 0.77 | 55 | empty |
| 3 | 198 | 0.52 | 0.78 | 30 | 7VI |
| 4 | 180 | 0.48 | 0.76 | 31 | 7VI |
| 5 | 155 | 0.44 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1712 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7RVO · Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI13 · 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 7RVO · PDBe 7RVO · UniProt P0DTD1
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