Skip to main content
. 2021 Mar 13;132:104325. doi: 10.1016/j.compbiomed.2021.104325

Table 3.

The binding potential of selected natural lead molecules towards the probable drug targets of human SARS-CoV-2 predicted by molecular docking studies.

Protein name PDB ID Ligand names Ligand structure Binding affinity (Kcal/mol) RMSD (Å) Interacting residues Hydrogen bonds
Spike glycoprotein 1WYY Hyoscyamine
Pubchem ID: 154417
Source: Datura stramonium 		Image 1 −8.14 0.0 Ser924, Thr925, Gly928, Asp932, Gln1161, ILe1164, Asn1168 (Chain A), Ser924, Thr925, Gly928, Gln1161, Ile1164 (Chain B) Asn1168: 2
Spike glycoprotein-Closed state 6VXX −5.7 0.0 Leu335, Pro337, Phe338, Gly339, Asp364, Val367 0
Spike glycoprotein-Open state 6VYB −6.0 0.0 Trp104, Ile119, Val126, Ile128, Tyr170, Ser172, Ile203, Val227 Ser172: 1
Membrane protein 3I6G −0.7 0.0 Gly0 0
Envelope small membrane protein 2MM4 −2.2 0.0 Lys63, Asn64 0
Replicase polyprotein 1 ab 1Q2W −6.1 0.0 Glu156, Met165, Asp187, Arg188, Gln189, Gln192 Gln192
Replicase polyprotein 1a 5RE4 −6.0 0.0 Trp218, Asn221, Leu271 Trp218: 1
Protein 7a 1XAK −4.4 0.0 Tyr3, Tyr5, His47, Gln61 0
Protein 9b 2CME −4.4 0.0 Arg68, Ala69, Phe70 0
Receptor binding domain of membrane protein 6M17 −5.4 0.0 Thr376, Val407, Ala411, Val433, Tyr508 0
Non-structural protein 7 6M71_C −5.3 0.0 Thr46, Phe49, Val53 0
Non-structural protein 8 6M71_B, D −5.9 0.0 Leu128, Val130, Thr141, Tyr149 0
Non-structural protein 12 6M71_A −5.4 0.0 Pro412, Phe415, Phe440, Phe843, 0
Non-structural Protein 6 Hypothetical model −5.2 0.0 Asp6, Phe7, Leu15, Leu40, Ile60 0
Non-structural Protein 10 Hypothetical model −6.1 0.0 Ile55, Cys74, Tyr76, His83, Asp91, Leu112, Thr115, Val116 His83:1
Protein 3a Hypothetical model −5.3 0.0 Phe56, Ile63, Lys66, Tyr189, Glu191, 0
Spike glycoprotein 1WYY Rotiorinol C
Pubchem ID: 11703984
Source: Chaetorium cupreum 		Image 2 −9.82 0.0 Arg4, Lys5, Tyr126, Gln127, Arg131, Asp289 and Glu290 5, Lys5, Gln127, Asp 289, Glu290 (A chain) Glu127 (B chain)
Spike glycoprotein-Closed state 6VXX −6.2 0.0 Arg34, Thr208, Pro209, Leu212, Pro217, Gln218, Phe220 Phe220: 1
Spike glycoprotein-Open state 6VYB −6.3 0.0 Thr33, Phe59, Asp287 0
Membrane protein 3I6G −0.6 0.0 Gly0 0
Envelope small membrane protein 2MM4 −2.2 0.0 Lys63, Asn64 0
Replicase polyprotein 1 ab 1Q2W −7.0 0.0 Phe3, Lys5, Arg131, Trp207, Phe291, Ile286, Asp289 Trp207: 1
Replicase polyprotein 1a 5RE4 −6.7 0.0 Lys137, Thr199, Tyr239, Leu286, Leu287, Glu288, Asp289 Tyr239, Asp289: 3
Protein 7a 1XAK −5.4 0.0 Tyr3, His47, Arg57, Thr59 0
Protein 9b 2CME −5.0 0.0 Ser56, Leu65, Glu66, Ala67, Arg68, Ala69, Phe70, Ser72 Ser56: 1
Receptor binding domain of membrane protein 6M17 −6.1 0.0 Cys336, Phe338, Gly339, Ala363, Asp364, Val367, Ser371, Ser373, Phe374, Ser373: 1
Non-structural protein 7 6M71_C −5.9 0.0 Lys2, Asp5, Thr9, Thr46, Phe49, Val53, Met52 0
Non-structural protein 8 6M71_B, D −6.0 0.0 Pro133, Asp134, Tyr135, Trp182, Pro178 Tyr135: 1
Non-structural protein 12 6M71_A −6.6 0.0 Arg181, Gln184, Asn213 0
Non-structural protein 6 Hypothetical model −5.6 0.0 Gln8, Lys38, Lys42, Leu44 Lys42: 1
Non-structural Protein 10 Hypothetical model −6.8 0.0 Ile55, His83, Lys96, Val116 His83:1
Protein 3a Hypothetical model −6.3 0.0 Phe28, Val29, Arg68, Ala72, Val90 0
Spike glycoprotein 1wyy Scutifoliamide A
Chemspider ID: 23311285
Source: Piper scutifolium 		Image 3 −6.4 0.0 Asn910, Ala940, Thr943, Leu944, Gln947, Asn951, Leu1178, Leu1181, Glu1183 0
Spike glycoprotein-Closed state 6VXX −5.4 0.0 Leu118, Val120, Phe135, Leu141, Leu241 0
Spike glycoprotein-Open state 6VYB −6.6 0.0 Phe823, Asn824, Val826, Pro863, Pro1057, His1058 Asn824: 1
Membrane protein 3I6G −0.7 0.0 Gly0 0
Envelope small membrane protein 2MM4 −0.8 0.0 Ly63 0
Replicase polyprotein 1 ab 1Q2W −6.9 0.0 Arg4, Lys5 and Phe291 (A chain), Lys 5 (B chain) 1; Lys5 (B chain)
Replicase polyprotein 1a 5RE4 −6.8 0.0 Val212, Arg217, Leu220, Gln256, Ile259, Asp263 0
Protein 7a 1XAK −5.6 0.0 Gln6, Cys8, Val9, Thr12, Leu16, Lys17 Val9, Lys17: 2
Protein 9b 2CME −4.4 0.0 Ala58, Arg68, Ala69, Phe70, Ser72 0
Receptor binding domain of membrane protein 6M17 −5.9 0.0 Gln493, Tyr495, Gly502, Tyr505 Gln493, Gly502: 2
Non-structural protein 7 6M71_C −5.9 0.0 Asp5, Thr9, Thr46, Phe49, Glu50, Val53 Thr9: 1
Non-structural protein 8 6M71_B, D −6.0 0.0 Leu128, Met129, Pro133, Thr141, Tyr149 0
Non-structural protein 12 6M71_A −6.1 0.0 Asp484, Ile488, Gln573, Ser578, Ala581 0
Non-structural Protein 6 Hypothetical model −5.5 0.0 Leu16, Ile17, Arg20, Thr21 Arg20: 1
Non-structural Protein 10 Hypothetical model −5.6 0.0 His83, Leu92, Asn114, Thr115, Val116 Val116: 2
Protein 3a Hypothetical model −5.4 0.0 Cys130, Trp131, His150, His204, His227 0
Spike glycoprotein 1wyy Tamaridone
Pubchem ID: 15345466
Source: Tamarix dioica 		Image 4 −7.2 0.0 Asp931, Asn935, Lys1162, Asp1165, Asn1168, Lys1172 1; Asn935
Spike glycoprotein-Closed state 6VXX −7.3 0.0 Ala520, Phe559, Phe562, Gln563, Gln564, Phe565, Gly566, Arg567 Gln564, Phe565, Arg567: 4
Spike glycoprotein-Open state 6VYB −6.8 0.0 Thr732, Thr778, Ser780, Pro863, His1058 Ser730: 2
Membrane protein 3I6G −0.8 0.0 Gly0 0
Envelope small membrane protein 2MM4 −3.1 0.0 Lys63, Asn64 Asn64: 1
Replicase polyprotein 1 ab 1Q2W −6.3 0.0 Gly11, Lys12, Glu14, Gly15, Gly11: 1
Replicase polyprotein 1a 5RE4 −7.0 0.0 Leu87, Lys137, Thr190, Tyr237, Tyr239, Leu285 Tyr237: 1
Protein 7a 1XAK −5.7 0.0 Val9, Thr12, Val14, Arg65 0
Protein 9b 2CME −5.6 0.0 Arg68, Gln71, Ser72 0
Receptor binding domain of membrane protein 6M17 −6.5 0.0 Thr345, Arg346, Ser349, Lys441, Lys444, Asn448, Asn450, Tyr451 Lys444: 1
Non-structural protein 7 6M71_C −5.9 0.0 Lys2, Val6, Thr9, Phe49, Met52 Thr9: 1
Non-structural protein 8 6M71_B, D −5.7 0.0 Leu128, Val130, Val131, Thr141, Tyr149 0
Non-structural protein 12 6M71_A −6.7 0.0 Lys47, His133, Asn138, Lys780 0
Non-structural Protein 6 Hypothetical model −5.6 0.0 Lys48, Ser50, Leu52, Asp53, Gln56 Leu52: 1
Non-structural Protein 10 Hypothetical model −6.7 0.0 Pro37, Asn105, Asp106, Phe110, Lys113, Asn114, Tyr126 Asn105, Asn114: 2
Protein 3a Hypothetical model −6.6 0.0 Gln213, Val255, Ile263, Thr270 0