MolNFT v1 · #181560 · protein
Crystal structure of the SARS-cov-2 (COVID-19) main protease in complex with inhibitor UAWJ9-36-3
7LYI · 3C-like proteinase: “Crystal structure of the SARS-cov-2 (COVID-19) main protease in complex with inhibitor UAWJ9-36-3”. X-ray diffraction, 2 ligands (YHI, NA), 2 pockets (best druggability 0.54). MolNFT v1 #181560 on GenesisL1: 3D…
- PDB
- 7LYI
- Type
- protein
- Length
- 304 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
- YHI, NA
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 26% helix, 28% strand | P0DTD1 |
Ligands and binding sites
- YHI · benzyl (1R,2S,5S)-2-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate · ligand · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.54 | 0.77 | 30 | YHI |
| 2 | 130 | 0.41 | 0.75 | 27 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7LYI · Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor… · 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 7LYI · PDBe 7LYI · UniProt P0DTD1
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