Research workbench
Structure of SARS-cov-2 3CL protease in complex with inhibitor 2C
Analyse Structure of SARS-cov-2 3CL protease in complex with inhibitor 2C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T42
- Type
- protein
- Length
- 599 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- FIK, FIW
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 298 | 25% helix, 30% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- FIK · (1S,2S)-2-[(N-{[(2-acetyl-2-azaspiro[3.3]heptan-6-yl) oxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · 2 copies · chains A, B
- FIW · (1R,2S)-1-hydroxy-2-{[N-({[2-(2-methylpropanoyl)-2-azaspiro[3.3]heptan-6-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.74 | 0.77 | 79 | empty |
| 2 | 96 | 0.54 | 0.84 | 22 | empty |
| 3 | 218 | 0.54 | 0.78 | 27 | FIK, FIW |
| 4 | 171 | 0.49 | 0.77 | 23 | FIK, FIW |
| 5 | 117 | 0.40 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 903 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7T42 · Structure of SARS-CoV-2 3CL protease in complex with inhibitor 2c · 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 7T42 · PDBe 7T42 · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.