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Crystal structure of the SARS-cov-2(2019-ncov) main protease in complex with compound 5
Analyse Crystal structure of the SARS-cov-2(2019-ncov) main protease in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L11
- Type
- protein
- Length
- 611 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
- XF1
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 24% helix, 28% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 27% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- XF1 · 2-[3-(3-chloro-5-propoxyphenyl)-2-oxo[2H-[1,3'-bipyridine]]-5-yl]benzonitrile · ligand · 2 copies · chains A, 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 | 863 | 0.76 | 0.79 | 73 | empty |
| 2 | 337 | 0.54 | 0.74 | 56 | empty |
| 3 | 224 | 0.53 | 0.77 | 33 | XF1 |
| 4 | 250 | 0.52 | 0.75 | 36 | empty |
| 5 | 193 | 0.49 | 0.76 | 29 | XF1 |
Interfaces
1 interface between chains.
- A–B · 1463 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 7L11 · Crystal structure of the SARS-cov-2(2019-ncov) main protease in complex with compound 5 · 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 7L11 · PDBe 7L11 · UniProt P0DTD1
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