MolNFT v1 · #181610 · protein
Structure of SARS-cov-2 3CL protease in complex with inhibitor 5C
7LZZ · 3C-like proteinase: “Structure of SARS-cov-2 3CL protease in complex with inhibitor 5C”. X-ray diffraction, 2 ligands (YMS, YMV), 1 pocket (best druggability 0.55). MolNFT v1 #181610 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7LZZ
- Type
- protein
- Length
- 299 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
- YMS, YMV
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 299 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- YMS · (1R,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1r,4S)-4-phenylcyclohexyl)oxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid · ligand · chains A
- YMV · (1S,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1r,4S)-4-phenylcyclohexyl)oxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.55 | 0.79 | 26 | YMS, YMV |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7LZZ · Structure of SARS-CoV-2 3CL protease in complex with inhibitor 5c · 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 7LZZ · PDBe 7LZZ · UniProt P0DTD1
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