MolNFT v1 · #169425 · protein
Crystal structure of the SARS-cov-2 (COVID-19) main protease in complex with inhibitor UAW248
6XBI · 3C-like proteinase: “Crystal structure of the SARS-cov-2 (COVID-19) main protease in complex with inhibitor UAW248”. X-ray diffraction, 4 ligands (UZ7, UZ4, UZ1), 6 pockets (best druggability 0.78). MolNFT v1 #169425 on GenesisL1…
- PDB
- 6XBI
- Type
- protein
- Length
- 615 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Inhibitor UAW248
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- UZ7, UZ4, UZ1, NA
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 307 | 25% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 25% helix, 29% strand | P0DTD1 |
| D, E | Inhibitor UAW248 | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- UZ7 · Phenyl hydrogen carbonate · ligand · 2 copies · chains A, D, B, E
- UZ4 · (2R,3S)-3-amino-2-hydroxy-4-[(3S)-2-oxopyrrolidin-3-yl]butanoic acid · ligand · 2 copies · chains A, D, B, E
- UZ1 · Cyclopropanamine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.78 | 0.80 | 84 | empty |
| 2 | 366 | 0.62 | 0.77 | 60 | DMS |
| 3 | 126 | 0.48 | 0.79 | 29 | UZ4, UZ1 |
| 4 | 148 | 0.43 | 0.75 | 25 | empty |
| 5 | 106 | 0.43 | 0.78 | 22 | UZ4, UZ1 |
Interfaces
3 interfaces between chains.
- A–B · 1526 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 279 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 263 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6XBI · Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor… · 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 6XBI · PDBe 6XBI · UniProt P0DTD1
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