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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