MolNFT v1 · #169424 · protein
Crystal structure of the SARS-cov-2 (COVID-19) main protease in complex with inhibitor UAW247
6XBH · 3C-like proteinase: “Crystal structure of the SARS-cov-2 (COVID-19) main protease in complex with inhibitor UAW247”. X-ray diffraction, 2 ligands (P6S, NA), 2 pockets (best druggability 0.37). MolNFT v1 #169424 on GenesisL1: 3D…
- PDB
- 6XBH
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Inhibitor UAW247
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- P6S, NA
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 26% helix, 28% strand | P0DTD1 |
| C | Inhibitor UAW247 | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- P6S · benzyl hydrogen carbonate · ligand · chains A, C
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.37 | 0.73 | 19 | empty |
| 2 | 60 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 359 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 6XBH · 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 6XBH · PDBe 6XBH · UniProt P0DTD1
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