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. 2015 Mar 27;9:1825–1841. doi: 10.2147/DDDT.S75886

Table 2.

Molecular docking analysis showing estimated binding energy, interacting residues, and molecular interactions of potential compounds in the binding site of HCV-NS5B

Ligand name Binding energy (kcal/mol) VdW interacting residues Number of H-bonds H-bonds interacting residues Number of direct contact (all polar, nonpolar interactions)
Naringenin −9.7 His428A, Val494, Leu392, Leu492, Ala395 3 Thr399, Arg503 36
Tryphanthrine −9.7 His428, Leu392, Leu492 3 Ala396, Ala395, Arg503 27
Dicoumarin −9.3 Ala395, Leu392, Val494 2 His428, Leu396 37
Swertianin −9.3 His428, Ala395, Leu392, Leu492 3 Cys146, Arg503, Ala396 26
Diosmetin −9.3 His428, Leu392, Val494 3 Ala396, Val37, Leu492 32
Apigenin −9.3 Leu492, Leu392, His428, Ala395 1 Cys146 35
Honokiol −9.3 Ala396, Ala395, His428, Val494, Leu392, Leu492 2 Leu492, Arg503 34
Luteolin −9.3 Val494, Leu392, Leu492 3 His428, Val37, Arg503 35
Thaliporphine −9.1 Ala395, His428, Leu392, Leu492, Pro495 3 Cys146, Ala396, Arg503 30
Oxymatrine −9 His428, Val494, Leu392, Ala396, Ala395, Pro495 1 Cys146, Arg503 31
Wedelolactone −8.9 Leu492, Leu392, His428 2 Ala396, Cys146 22
Desmethylwedelolactone −8.9 His428, Leu392, Leu492 3 Ala396, Cys146 27
Berberine −8.9 Ala396, His428, Leu392, Val494, Leu492 1 Thr399 30
Andrographolide −8.9 Ala395, His428, Leu392, Val494, Leu492 2 Cys146, Ala396 29
Ladanein −8.9 Ala396, Leu392, Val494, Leu492 2 His428, Cys146 33
Curcumin −8.8 Leu492, Ala396, Leu392, Leu492, Pro495 2 His428, Cys146 41
Genistein −8.8 Leu492, Ala396, Ala395, Leu392, Val494 2 His428, Arg503 29
Loganin −8.7 His428, Leu392 2 Ala396 25
Epicatechin −8.6 His428, Leu392, Ala396 2 Cys146, Arg503 34
Hypophyllanthin −8.6 Leu492, Leu392 2 Arg503 32
Quercetin −8.5 Val494, Leu492 1 Ala396 29
Silymarin/silibinin −8.5 Pro495, Ala396, Arg503, Ala395 4 His428, Arg503 40
Phyllanthin −8.4 His428, Arg503, Leu392, Pro495, Val494, Leu492, Ala396, Ala395 0 n/a 42
Lucidone −8.3 His428, Leu392, Val494, Leu492 3 Cys146, Ala395, Ala396 35
Jatrorrhizine −8.3 Ala396, Leu392, Val494, Leu492 2 Cys146, His428 21
Caruilignan C −8.1 Ala396, His428, Leu392, Val494, Leu492 1 Cys146, Arg503 34
Verbenalin −8.1 His428, Pro495, Val494, Leu492 4 Cys146, Arg503, Ala396 33
Geranyl acetone −8.1 His428, Leu392, Leu492, Val494, Ala396, Ala395 0 n/a 36
Nobiletin −7.8 Ala396 2 Leu492 29
Tetradecanoic acid −7.4 Ala396, His428, Leu392, Val494, Leu492 1 Arg503 24
Sofosbuvir −6.2 Ala395, Ile424, Ala396, Val494, Leu492, His428 2 Arg503, Thr399 26

Abbreviations: HCV, hepatitis C virus; NS5B, nonstructural protein 5B; n/a, not available.