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Crystal structure of SARS-CoV-2 3CL protease in complex with a dimethyl sulfinyl benzene inhibitor
Analyse Crystal structure of SARS-CoV-2 3CL protease in complex with a dimethyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8E5X
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- UO9, URR
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.7 · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 299 | 26% helix, 30% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 27% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- UO9 · (2~{S})-2-[[(2~{S})-4-methyl-2-[[2-methyl-2-[oxidanyl(phenyl)-$l^{3}-sulfanyl]propoxy]carbonylamino]pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic acid · ligand · 2 copies · chains A, B
- URR · N~2~-(ethoxycarbonyl)-N-{(1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-sulfanylpropan-2-yl}-L-leucinamide · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.74 | 0.78 | 80 | empty |
| 2 | 195 | 0.54 | 0.78 | 35 | empty |
| 3 | 214 | 0.52 | 0.77 | 29 | UO9, URR |
| 4 | 194 | 0.52 | 0.78 | 27 | UO9, URR |
| 5 | 75 | 0.32 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 938 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
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 8E5X · PDBe 8E5X · UniProt P0DTD1
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