2021 Jan 4;38(1):71–86. doi: 10.1007/s42600-020-00122-3

Table 2.

Result of 6vyb molecular docking with all ligands, which are under study in this work. Five ligand groups are ranked by binding affinity

Ligand name	Chemical formula	Binding affinity (kcal/mol)	Residue interaction with ligand through hydrogen binding	Residues interaction with ligand through hydrophobic binding
Anti-viruses
Indinavir	C₃₆H₄₇N₅O₄	−8.1	Asn241, Asn335	Phe240, Phe272, Leu339
Maraviroc	C₂₉H₄₁F₂N₅O	−8	G424	Phe227, Ile230, Thr231, Asp287, Lys426
Raltegravir	C₂₀H₂₁FN₆O₅	−8	Ser269, Trp334, Arg407	Val265
Saquinavir	C₃₈H₅₀N₆O₅	−7.7	Ser264, Pro425	Val225, Ile230, Lys427
Methylprednisolone	C₂₂H₃₀O₅	−7.6	Arg253, Thr328, Gln414	Phe362
Etravirine	C₂₀H₁₅BrN₆O	−7.5	Ser271	Phe240, Asn241, Phe272, Trp334, Leu339
Acteoside	C₂₉H₃₆O₁	−7.3	Phe240, Asn241, Asn335, Asn338, Gln404	Phe272, Trp334
Cyclosporin A	C₆₂H₁₁₁N₁₁O₁₂	−7.2	Arg253	Phe290, Tyr294, Phe327, Thr328, Phe362, Leu415, Leu416
Nelfinavir	C₃₂H₄₅N₃O₄S	−7.1	Thr421, Cys423	Phe227, Pro228, Ile230, Thr231, Val260, Lys426
Efavirenz	C₁₄H₉ClF₃NO₂	−7	Thr328	Tyr294, Pro324, Phe362
Aldosterone	C₂₁H₂₈O₅	−6.9	Arg253, Thr328, Glu414	Phe362
Delavirdine	C₂₂H₂₈N₆O₃S	−6.9	Asn258	Phe227, Asn258
Alclometasone	C₂₂H₂₉ClO₅	−6.8	Thr328, Pro361, Phe362	Phe362, Glu414
Abacavir	C₁₄H₁₈N₆O	−6.7	Ser269. Ser271	Val265, Leu266, Phe272
Atazanavir	C₃₈H₅₂N₆O₇	−6.6	Arg253	Phe290, Tyr294, Phe328, Phe362, Leu415, Leu416
Imiquimod	C₁₄H₁₆N₄	−6.6	–	Leu266, Phe272, Trp334
Lopinavir	C₃₇H₄₈N₄O₅	−6.6	Cys259	Phe227, Pro228, Ile230, Thr231, Asn258, Val260, Lys426
Entecavir	C₁₂H₁₅N₅O₃	−6.5	Cys259	–
Sofosbuvir	C₂₂H₂₉FN₃O₉P	−6.5	Cys259, Asn442	Phe227, Pro228, Ile230, Asn258, Thr421, Lys426
Zidovudine	C₁₀H₁₃N₅O₄	−6.4	Ala420, Gly424	–
Stavudine	C₁₀H₁₂N₂O₄	−6.3	Ser269, Ser271	Phe240, Phe272, Phe272, Leu339
Telbivudine	C₁₀H₁₄N₂O₅	−6.3	Ser271, Arg407	Phe240, Phe272, Trp334, Leu339
Zalcitabine	C₉H₁₃N₃O₃	−6.3	Ser271	Phe240, Leu266, Trp334
Didanosine	C₁₀H₁₂N₄O₃	−6.1	Phe240, Asn241, Ser269, Ser271	Phe272
Nevirapine	C₁₅H₁₄N₄O	−6.1	–	Phe240, Phe272, Trp334
Ribavirin	C₈H₁₂N₄O₅	−6.1	Arg352, Arg355, Ser367, Gln369	–
Telaprevir	C₃₆H₅₃N₇O₆	−6.1	–	Phe227, Pro228, Ile230, Val260, Lys426, Asn442
Emtricitabine	C₈H₁₀FN₃O₃S	−6	Cys259, Thr421, Gly424, Lys426	–
Ganciclovir	C₉H₁₃N₅O₄	−5.9	Phe240, Trp334, Arg407	Ala242, Ser269, Ser271, Arg407
Fosamprenavir	C₂₅H₃₆N₃O₉PS	−5.8	Thr231	Phe227, Pro228, Val260,Lys426
Penciclovir	C₁₀H₁₅N₅O₃	−5.8	Phe227, Pro228, Asp262, Lys426	Ile230, Pro425, Lys427
Rimantadine	C₁₂H₂₁N	−5.8	Cys234, Gly237	Leu233, Phe236, Val265, Leu266
Lamivudine	C₈H₁₁N₃O₃S	−5.7	Pro228, Cys259, Thr421, Gly424, Lys426	Thr231
Valganciclovir	C₁₄H₂₂N₆O₅	−5.7	–	Phe240, Ser269, Ser271
Aciclovir	C₈H₁₁N₅O₃	−5.6	Phe240, Asn241, Ser269, Ser271	–
Gancyclovir	C₉H₁₃N₅O₄	−5.6	Phe240, Asn241	–
Ritonavir	C₃₇H₄₈N₆O₅S₂	−5.6	–	Pro228, Thr231, Val260, Asn442
Tenofovir	C₉H₁₄N₅O₄P	−5.6	Trp334	Phe272, Trp334
Valaciclovir	C₁₃H₂₀N₆O₄	−5.6	Asn241, Ser269, Trp334	Leu339
Famciclovir	C₁₄H₁₉N₅O₄	−5.5	Ala420	Phe227, Ile230, Thr231, Val260
Idoxuridine	C₉H₁₁IN₂O₅	−5.5	Trp334	–
Oseltamivir	C₁₆H₂₈N₂O₄	−5.5	Asp318, Thr328, Ser412	Pro324, Thr328, Phe362, Glu414
Zanamivir	C₁₂H₂₀N₄O₇	−5.5	Arg226, Ser428, Gln478	–
Amantadine	C₁₀H₁₇N	−5.3	Pro228, Asn229	Val260, Lys426
Docosanol	C₂₂H₄₆O	−3.8	–	Ile230, Leu233, Phe236, Val265, Leu266, Pro425
Methoxyethanol	C₃H₈O₂	2.9	Arg352, Lys356, Ser367, Glu369	–
Enfuvirtide	C₂₀₄H₃₀₁N₅₁O₆₄	−2.2	Ser257	–
Drug of cov2
Baloxavir marboxil	C₂₇H₂₃F₂N₃O₇S	−7.7	–	Phe227, Pro228, Ile230, Thr231, Lys426, Asn442
Indomethacin	C₁₉H₁₆ClNO₄	−7	Pro228	Ile230, Thr231, Val260, Lys426
Azvudine	C₉H₁₁FN₆O₄	−6.2	Cys423, Gly424, Lys426	–
Oseltamivir	C₁₆H₂₈N₂O	−5.4	Thr328, Ser412	Pro324, Thr328, Pro361, Phe362, Glu414
Chloroquine	C₁₈H₂₆ClN₃	−5.3	THR328	Tyr294, Thr328, Pro361, Phe326, Glu414
Favipiravir	C₅H₄FN₃O₂	−5	Val239, Ala246, Asn252, Ser297
Flavonoids
Ononin	C₂₂H₂₂O₉	−7.8	Thr283, Asp287, Lys427	Ile230, Pro425
Genistein	C₁₅H₁₀O₅	−7.3	Asn338	Phe272, Leu339
Luteolin	C₁₅H₁₀O₆	−7.2	Ser273, Thr274, Tyr278, Tyr406	Lys276, Val305, Arg306
Morin	C₁₅H₁₀O₇	−7.2	Asn241, Asn338	Phe240
Fisetin	C₁₅H₁₀O₆	−7.1	Asp326, Thr328, Pro361, Phe413	Pro324, Pro361
Taxifolin	C₁₅H₁₂O₇	−7.1	Ala242, Trp334, Arg407	Phe240, Asn241, Phe272, Trp334, Leu339
Galangin	C₁₅H₁₀O₅	−7	Asn241, Asn338	Phe240
Isorhamnetin	C₁₆H₁₂O₇	−6.9	Ser269, Asn338	Phe240, Phe272
Naringenin	C₁₅H₁₂O₅	−6.8	Ala242, Trp334, Arg407	Phe240, Asn241, Phe272, Trp334, Leu339
Quercetin	C₁₅H₁₀O₇	−6.6	Asp326, Thr328, Phe413	Pro361, Phe362
Fluorophenyl
1,2-Ethanediol,1,2-bis(4-fluorophenyl)	C₁₄H₁₂F₂O₂	−6.7	Gly394	Asn319, Tyr393 Tyr403
1,1-bis(3-Fluorophenyl)-2-methoxyethanol	C15H14F2O2	−6.6	Gly394, Gln396 Asn399, Gly400	Tyr393, Tyr403
Phenylpropanoid
Telmisartan	C₃₃H₃₀N₄O₂	−8.8	Asp262	Val260, Ala261, Gly424,Pro425, Lys426,Lys427
Sennoside	C₄₂H₃₈O₂₀	−8.6	Arg253, Asp326, Thr328, Ser412, Arg364	Phe327, Lys360, Pro361,Phe362,Phe413, Glu414
Glycyrrhizic acid	C₄₂H₆₂O₁₆	−8.3	Pro228, Cys259, Cys423, Thr421, Lys426	Phe227, Asn229, Ile230,Arg287, Leu288, Cys289, Ala420, Val422
Verbascoside	C₂₉H₃₆O₁₅	−8.1	Val239, Ser247, Asn252, Ala250, Ser297, Asn348	Arg244, Phe245, Ala246, Trp251, Tyr349, Leu350
Orobanchoside	C₂₉H₃₆O₁₆	−8	Cys259, Ala420, Thr421, Cys423,	Trp334, Asn335, Ser336, Asn337, Asn338, Ala270, Ser271, Phe274, Ser273
Arenarioside	C₃₄H₄₄O₁₉	−7.9	Pro228, Asn229, Thr421, Lys426, Asn442, Cyx259, Gln462	Phe227, Ile230, Asn258, Cys259, Val260, Val422, Cys423, G424, Pro425
Isomartynoside	C₃₁H₄₀O₁₅	−7.8	Ser264, Pro425	Gly424, Lys426, Lys427, Ser428, Val260, Ala261, Asp262
Poliumoside	C₃₅H₄₆O₁₉	−7.8	Thr421, Pro228, Cys259	Phe227, Asn229, Ile230, Asn258, Val260, Asp287, Leu288, Cys289, Val422, Cys423, Gly424
Teucrioside	C₃₄H₄₄O₁₉	−7.7	Asp262, Ser264, Pro425, Ser428, Gln478	Phe227, Pro228, Asn229, Ile230, Gly424, Lys426, Lys427
Angoroside A	C₃₄H₄₄O₁₉	−7.7	Cyx259, Gln462, Pro477	Asn258, Val260
Pheliposide	C₃₆H₄₆O₂₀	−7.6	Asn232, Leu233, Gly237, Asn241, Thr243, Asp262	Cys234, Pro235, Phe236, Ala 242, Val260, Ala261
Rutin	C₂₇H₃₀O₁₆	−7.5	Arg253, Asp326, Thr328, Pro361, Arg364, Phe413, Gln414	Phe327, Gly329, Ser412
Forsythoside B	C₃₄H₄₄O₁₉	−7.5	Pro228, Cys259, Lue288, Ala420, Cys423, Gly424, Lys426	Pro228
Rossicaside A	C₃₅H₄₆O₂₀	−7.4	Gln238, Val239, Ser247, Thr249, Trp251, Asn252, Arg253, Ser297	Lys249, Ala250, Tyr347, Asn348, Tyr349, Leu350
Forsythiaside A	C₂₉H₃₆O₁₅	−7.4	Phe240, Asn241, Ala270, Ser271, Phe272, Asn335, Asn338, Tyr406	Ser273, Trp334, Ser336, Asn337, Val401
Purpureaside C	C₃₅H₄₆O₂₀	−7.4	Leu288, Ala420, Thr421, Gln462	Phe227
Hesperidin	C₂₈H₃₄O₁₅	−7.4	Pro228, Cys259, Thr421, Lys426	Phe227, Val260
Isoverbascoside	C₂₉H₃₆O₁	−7.4	Ala244, Ser247, Trp251, Asn252, Ser297, Asn348	Ala246, Phe245, Tyr249, Ala250
Leucosceptoside A	C₃₀H₃₈O₁₅	−7.4	Asp326, Thr328, Pro361, Glu414, Leu415	Tyr294, Pro 324, Phe362, Leu415
Corosolic acid	C₃₀H₄₈O₄	−7.3	Ser273, Thr406	Val305, Arg306, Ala309, Val401, Tyr406
Calceolarioside C	C₂₈H₃₄O₁₅	−7.2	Asn241, Ser271, Ser296, Trp334, Asn335, Asn338	Asn241
Eukovoside	C₃₀H₃₈O₁₅	−7.2	Val239, Phe245, Ser247, Asn348, Ser297	Tyr249, Ile366, Thr368
Angoroside C	C₃₆H₄₈O₁₉	−7.1	Asn229, Pro228, Thr231, Cys259, Thr421, Cys423, Lys426	Phe227, Pro228, Val260
Conandroside	C₂₈H₃₄O₁₅	−7.1	Gln238, Ala250, Trp251, Asn252, Ser247, Ser297, Asn348	Ala250, Ile366
Losartan	C₂₂H₂₃ClN₆O	−7.1	Ser273, Arg306	Thr274, Lys276, Val305, Arg306, Val331, Val401
Martynoside	C₃₁H₄₀O₁₅	−7.1	Ala246, Ser247, Asn252, Ser297, Asn348	Tyr249, Ile366
Suspensaside	C₂₉H₃₆O₁₆	−7.1	Arg253, Thr328, Lys360, Arg364, Phe413, Glu414	Tyr294, Phe362
Cistanoside D	C₃₁H₄₀O₁₅	−7	Thr328, Phe413, Gly414, Leu415	Tyr294, Pro324, Pro361, Phe362,Leu415
Osmanthuside B	C₂₉H₃₆O₁₃	−7	Cys259, Ala420, Thr421, Cys423	Phe227, Pro228, Thr231, Val260, Lys426, Pro477
Tubuloside A	C₃₇H₄₈O₂₁	−6.9	Arg253, Thr328, Asp326, Phe362, Arg364	Pro324, Phe362, Glu363, Glu414
Grayanoside B	C₂₆H₄₂O₉	−6.9	Cys259, Thr421, Asn442	Phe227, Thr231, Lys426
Campneoside	C₃₀H₃₈O₁₆	−6.7	Pro228, Asn229, Cys259, Val260, Cys423 Gly424	Val260
Cistanoside C	C₃₀H₃₈O₁₅	−6.7	Pro228, Asn229, Cys259, Cys423	Phe227, Val260
Grayanoside A	C₂₄H₂₈O₁₀	−6.7	T328, Pro361, Phe413	Tyr294, Pro324, Phe362
Oleuropein	C₂₅H₃₂O₁₃	−6.5	Thr231, Asn258, Leu288, Ala420, Gly424	THE231
Tubuloside C	C₃₇H₄₈O₂₁	−6.3	Arg253, Thr325, Arg364	Pro324, Pro361, Phe362, Glu414, Leu416
Salidroside	C₁₄H₂₀O₇	−6.1	Ala242, Ser269, Thr334, Arg407	Phe240, Trp334
Propane
1,2-Propanediol,3,3,3-trifluoro-2-phenyl-(2R)	C9H9F3O2	−6.7	Gly394	Tyr393, Asn399 Tyr403
1,1-Diphenyl propane-1,2-diol	C₁₆H₁₈O₂	−6.4	Gly394, Asn399	Arg301, Tyr393 TYR403
(S)-1,1-Diphenylpropane-1,2-diol	C15H16O2	−6.2	Gly394, Gln396 Asn399	Tyr393, Tyr403