MolNFT v1 · #178929 · protein
Structure of the SARS-cov-2 main protease in complex with inhibitor MPI6
7JQ3 · 3C-like proteinase: “Structure of the SARS-cov-2 main protease in complex with inhibitor MPI6”. X-ray diffraction, 1 ligand (VHP), 3 pockets (best druggability 0.55). MolNFT v1 #178929 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7JQ3
- Type
- protein
- Length
- 306 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- VHP
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 25% helix, 28% strand | P0DTD1 |
Ligands and binding sites
- VHP · N-[(benzyloxy)carbonyl]-O-tert-butyl-L-threonyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.55 | 0.78 | 29 | VHP |
| 2 | 84 | 0.34 | 0.75 | 18 | empty |
| 3 | 62 | 0.29 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 2 modified, 1 covalent (oxidation, covalent ligand).
Compared structures
- 7JQ3 · Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI6 · 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 7JQ3 · PDBe 7JQ3 · UniProt P0DTD1
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