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. 2018 Dec 8;4(12):e01023. doi: 10.1016/j.heliyon.2018.e01023

Table 1.

Summary of molecular interactions of panduratin A and 14 derivatives (100 docking runs).

Compound NS2B/NS3 protease residue
FEB (kcal/mol) Estimated Inhibition Constant, Ki (μM)
Hydrogen bonding
Hydrophobic interactions
S1 S2 S3 S4 Others S1 S2 S3 S4 Others
Panduratin A G151, G153, D81, G82 S135(2), Y150, Y161(5) D75, N152(7) V154(2) H51(2), D81, G82(2), S83, M84, F130, G151(3), G153(8), V155(2) -6.93 8.36
Diversity 0713 N152 G151, G153 Y150, Y161 -6.64 13.49
1 S135 F130, S131 D129(3), S135(2), Y150(4), Y161(7) F130(4), S131(2), P132(3), T134(3), G151(2) -4.80 303.19
2 N152 G151, G153 S135(3), Y150, Y161(9) N152(6) V154(2) H51, P132, G151(3), G153(4), V155(2) -5.51 91.38
3 N152 G151, G153 135(3), Y150(1), Y161(8) N152(6) V154 H51, M84, I86, F130(3), S131(2), P132(3), G151(6), G153(7), 155(4) -6.37 21.49
4 N152 G151, G153 S135(2), Y150, Y161(8) N152(5) H51, F130(2), S131, G151(7), G153(3) -6.03 37.89
5 N152 G151, G153 S135(2), Y150(2), Y161(8) N152(6) V154(2) H51, M84, F130(3), S131, T134, G151, G153(5), V155(2) -7.52 3.08
6 S135 N152 G151, G153, V155 S135, Y150, V154(3), Y161(8) N152(6) M84, S131, P132, G151(4), G153(5), V155(2) -5.06 195.64
7 N152 G151, G153, P132 S135(2), Y150(2), Y161(8) N152(4) V154(2) F130(2), S131(2), P132(2), T134(2), G151(2), G153(7), V155(2) -6.42 19.72
8 N152 G151, G153 S135(2), Y150(2), Y161(9) N152(5) V154(2) P130(3), S131(3), P132(2), T134(2), G151(2), G153(7), V155(2) -6.79 10.54
9 N152 G151, G153 S135, Y150(3), Y161(7) N152 (5) V154 S83(2), M84(2), P130(3), S131(3), P132(2), T134(2), G151, G153(7), V155 -7.10 6.29
10 S135 S135 (5), Y150, Y161(7) N152 I36(2), V52, F130, S131, P132(4), G151(5), G153(4), V155(2) -7.53 3.02
11 Y161 G151 S135(5), Y150(2), Y161(6) D75(3), N152 I36(2), W50(2), H51(16), V52, V72(2), D81(2), G82(2), F130(2), S131(2), P132(4), T134, G151(2), G153, V155 -8.88 0.311
12 Y161 G151, G153, W50, G82, M84 Y161 D75(2), N152(7) W50(3), H51, V72(4), D81(7), G82, S83, M84, G151(3), G153(3) -6.90 8.70
13 Y161 G151, G153, W50, G82, M84 Y161 D75(2), N152(6) W50 (5), V72 (4), D81 (8), G82, S83 (2), M84, G151 (3), G153 -6.51 16.86
14 S135, D129 G153, F130, T134 S135(3), Y150(4), Y161(7) N152(6) S83(2), M84, F130(3), S131(2), T134(2), G151(4), G153(5) -6.94 8.16

Sub-pocket residues: S1 (D129, S135, Y150, Y161), S2 (D75, D82, G83, N84, N152), S3 (F85, Q86, L87), S4 (V154), Catalytic triad (H51, D75, S135). *Number in bracket ( ) represent the number of hydrophobic interactions formed.