Research workbench
Covalent complex of SARS-CoV main protease with 4-methoxy-N-[(2S)-4-methyl-1-oxo-1-({(2S)-3-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)pentan-2-yl]-1H-indole-2-carboxamide
Analyse Covalent complex of SARS-CoV main protease with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XHN
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.377
- Source
- Human SARS coronavirus
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0C6U8
- Ligands
- V3D
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · resolution 1.377 · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 26% helix, 30% strand | P0C6U8 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 25% helix, 29% strand | P0C6U8 |
Ligands and binding sites
- V3D · (3S)-3-{[N-(4-methoxy-1H-indole-2-carbonyl)-L-leucyl]amino}-2-oxo-4-[(3S)-2-oxopyrrolidin-3-yl]butyl 2-cyanobenzoate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.70 | 0.77 | 91 | empty |
| 2 | 752 | 0.69 | 0.76 | 59 | EDO |
| 3 | 186 | 0.50 | 0.77 | 23 | V3D |
| 4 | 177 | 0.48 | 0.76 | 23 | V3D |
| 5 | 119 | 0.39 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1124 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6XHN · Covalent complex of SARS-cov main protease with 4-methoxy-N-[(2S)-4… · 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 P0C6U8
- Elsewhere: RCSB PDB 6XHN · PDBe 6XHN · UniProt P0C6U8
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