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Table 4 Protein residue interactions with the compounds and Remdesivir

From: In silico identification of compounds from Nigella sativa seed oil as potential inhibitors of SARS-CoV-2 targets

Protein–ligand complex Interacting residues
Hydrogen bond Unfavorable donor–donor Pi-sigma Pi-alkyl Alkyl Carbon–hydrogen Attractive charge
3CLpro-Caryopyellene oxide PHE294
3CLpro-Remdesivir SER158; THR111 SER158; THR292 1LE249; PRO293
ACE2- β-bisabolene HIS450; LYS541; LYS441 HIS540; PRO415; PHE438; ILE291
ACE2-Remdesivir GLU398; ALA348; ASP350 TRP349 TRP349; ARG393 GLU402; ALA348; ASP382 ASP382; ASP350
NSP3-Cryophyllene oxide ALA129
NSP3-Remdesivir ASP157; PHE156 PHE156 GLY48; PHE156 ALA38; ILE131 VAL49; ALA52 LEU126
NSP9-Cryophyllene oxide ILE68
NSP9-Remdesivir PRO58; SER60 ARG40 VAL42; PHE56 ILE66 ARG40
RDRP-Cryophyllene oxide ASN209
RDRP-Remdesivir ASN52; THR206; ASN209; ASP208 ILE37 ASP218
RP1A- α-bergamotene ˗ ILE120; ALA150; ALA102; LEU122
RP1A-Remdesivir ILE120; ILE106 PRO116; ILE119; ILE107; LEU95; LEU103 ILE120; ILE106; ALA150; ALA102