Table 5.

Specific binding site for a particular drug ligand for a specific protein with binding energy less than −7.5 kcal/mol. Binding site was compared with active site and common amino acids are listed.

Sr. No.	Active site	Name of the drug with binding energy in –Kcal/mol	Binding with drug with binding energy
1.	6Y84 (Mpro/3CLpro (Main protease of SARS-CoV-2)) MET6, ALA7, PHE8, PRO9, VAL104, ILE106, GLN107, PRO108, GLY109, GLN110, THR111, GLN 127, PRO132, ASN151, ILE152, ASP153, TYR154, CYS156, SER158, ILE200, THR201, VAL202, ASN203, GLU240, PRO241, ASP245, HIS246, ILE 249, GLU290, PHE291, THR292, PRO293, PHE294, ASP295, ARG298, GLN299, GLY302, VAL303, THR304	Lopinavir (−9.9) GLN 127, GLU290, PHE291
		Remdesivir (−9.4) GLN 127, GLU290, PHE291
		Eriodictyol (−8.8)
		GLN 127, GLU290
		Ritonavir (−8.7) GLN 127, GLU290, PHE291
		Ribavirin (−8.2) GLN127, GLU290
		Pemirolast (−8.2) GLN127, GLU290
		Mycophenolic acid (−8) GLN127, GLU290
		Hydroxychloroquine (−7.9) GLN 127, GLU290, PHE291
		Chloroquine (- 7.8) GLU290, PHE291
2	6VXS (ADP ribose phosphatase of NSP3 from SARS CoV-2) ALA21, ASP22, ILE23, VAL24, ALA38, ALA39, ASN40, LYS44, GLY46, GLY47, GLY48, VAL49, ALA50, ALA52, VAL95, GLY97, PRO125, LEU126, LEU127, SER128, ALA129, GLY130, ILE131, PHE132, PRO136, ALA154, VAL155, PHE156, ASP157, LEU160	Lopinavir(-7.9) LYS44
		Eriodictyol (−7.8) ALA38, ASN40, GLY46, GLY47, GLY48,VAL49, ALA50, PRO125, LEU126, LEU127, SER128, ALA129, ILE131, PHE132
		Pemirolast (−7.6) LYS44
3	6M03 (COVID-19 main protease in apo form) CYS 22, GLY23, THR24, THR25, THR26, LEU27, HIS41, VAL42, ILE43, CYS44, THR45, SER46, MET49, LEU50, LYS61, PHE140, LEU141, ASN142, GLY143, SER144, CYS145, HIS163, HIS164, MET165, GLU166, LEU167, PRO168, ARG188, GLN189, THR190, GLN192	Remdesivir (−7.8)
		Pemirolast (−7.7)
4	2GHV (SARS spike protein receptor binding domain) Chain E PHE361, SER362, THR363, PHE364, LYS365, CYS366,TYR367, GLY368, GLY391, ASP392, VAL394, ARG395, ILE397, ALA398, PRO399, GLN401, ASP414, PHE416, VAL420, ALA422, ILE489, GLY490, TYR494 Chain C PHE361, SER362, THR363, PHE364, LYS365, CYS366, TYR367, GLY368, GLY391, ASP392, VAL394, ARG395, ILE397, ALA398, PRO399,GLY400, GLN401, ASP414, PHE416, VAL420, ALA422, ILE489, GLY490, TYR494	Ritonavir (−7.6) Chain E PHE361, SER362 Chain C GLY368
5	6VSB C (Spike glycoprotein) Active site contains many amino acids	Eriodictyol (−7.6) ASN544, VAL576, PHE543, LEU546, PHE565, ALA522, ARG577, PRO521, PRO579, GLN564
6	6W75A (NSP10 – NSP16 Complex from SARS-CoV-2) ASN6841, LYS6844, TYR6845, HIS6867, PHE6868, GLY6869, ALA6870, GLY6871, SER6872, ASP6873, PRO6878, GLY6879, SER6896, ASP6897, LEU6898, ASN6899, ASP6900, PHE6901, GLY6911, ASP6912, CYS6913, ASP6928, MET6929, TYR6930, ASP6931, PRO6932, LYS6933, GLY6946, PHE6947, LYS6968	Eriodictyol (−7.8)
7	6W75C (NSP10 – NSP16 Complex from SARS-CoV-2) ASN6841, LYS6844, TYR6845, HIS6867, PHE6868, GLY6869, ALA6870, GLY6871, SER6872, ASP6873, PRO6878, GLY6879, SER6896, ASP6897, LEU6898, ASN6899, ASP6900, PHE6901, GLY6911, ASP6912, CYS6913, ASP6928, MET6929, TYR6930, ASP6931, PRO6932, LYS6933, GLY6946, PHE6947, LYS6968	Remdesivir (−7.6)
		Eriodictyol (−7.5)
8.	6W75D (NSP10 – NSP16 Complex from SARS-CoV-2) ALA4273, VAL4274, ASP4275, ALA4276, ALA4277, TYR4329, ILE4334, ASP4335, HIS 4336, PRO4337	Eriodictyol (−7.5) TYR4329, HIS 4336, PRO4337
9	6M18B (Angiotensin-converting enzyme 2 (ACE2) receptor) SER623, LYS625, SER626, ALA627, LEU628, GLY629, ASP630, LYS631, ARG678, ARG705, ARG708, SER709, ASN712, ASP713, ARG716, LEU717, ASN718, ASP719, ASN720, SER721, GLU723, ILE727, GLN728, PRO729, THR730, LEU731, GLY732, PRO733, PRO734, ASN735, GLN736, PRO737, PRO738, VAL739, ILE741, ILE744, VAL745, VAL748, VAL749, VAL752, ILE753, VAL755, GLY756, VAL758, ILE759, LEU760, PHE762, THR763, ARG766, ASP767, ARG768, SER623	Lopinavir (−8.6)
		Ritonavir(-8.2)
		Remdesivir (−8.2)
		Eriodictyol (−7.5)
10	6M18D (Angiotensin-converting enzyme 2 (ACE2) receptor) SER623, LYS625, SER626, ALA627, LEU628, GLY629, ASP630, LSY631, ARG678, ARG705, ARG708, SER709, ASN712, ASP713, ARG716, LEU717, ASN718, ASP719, ASN720, SER721, GLU723, ILE727, GLN728, PRO729, THR730, LEU731, GLY732, PRO733, PRO734, ASN735, GLN736, PRO737, PRO738, VAL739, ILE741, ILE744, VAL745, VAL748, VAL749, VAL752, ILE753, VAL755, GLY756, VAL758, ILE759, LEU760, PHE762, THR763, ARG766, ASP767, ARG768	Lopinavir (−8.9)
		Ritonavir (−8.1)
		Remdesivir (−7.7)