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Table 2 Binding free energy components of protein-protein and protein-ligand complexes (in kcal/mol units)

From: KRas4B-PDE6δ complex stabilization by small molecules obtained by virtual screening affects Ras signaling in pancreatic cancer

System

ΔEvdw

ΔEele

ΔGele,sol

ΔGnpol,sol

ΔEnon-polar

ΔEpolar

ΔGbind

Protein-protein Free and bound wild type KRas4B-PDE6δ complex

 KRas4B-PDE6δ

− 123.08 (0.35)

− 1546.94 (4.40)

1608.17 (4.25)

−17.78 (0.04)

− 140.86

61.23

−79.63 (0.43)

 KRas4B-PDE6δ-D14

− 124.99 (0.44)

− 1127.75 (3.74)

1187.01 (3.50)

− 18.26 (0.05)

− 143.25

59.26

−83.99 (0.42)

 KRas4B-PDE6δ-C22

− 142.17 (0.40)

− 1113.87 (4.30)

1185.59 (4.11)

−20.62 (0.03)

− 162.79

71.72

−91.07 (0.38)

Free and bound mutated KRas4BG12C-PDE6δ

 KRas4BG12C-PDE6δ

−127.74 (0.51)

− 1507.30 (5.58)

1550.55 (5.31)

−18.85 (0.06)

− 146.59

43.25

− 103.34 (0.77)

 KRas4BG12C-PDE6δ-D14

−124.12 (0.51)

− 1083.80 (6.00)

1142.97 (5.68)

−18.00 (0.05)

−142.12

59.17

−82.95 (0.68)

 KRas4BG12C-PDE6δ-C22

− 126.67 (0.39)

− 1550.02 (3.88)

1587.85 (3.75)

−18.86 (0.05)

− 145.53

37.83

−107.70 (0.50)

Protein-ligand

 PDE6δ-D14

−47.22 (0.15)

− 120.27 (0.95)

134.17 (0.86)

− 6.40 (0.02)

−53.62

13.90

−39.72 (0.20)

 PDE6δ-C22

−41.76 (0.15)

−173.27 (0.47)

163.16 (0.38)

−6.54 (0.01)

−48.30

−10.11

− 58.41 (0.19)

  1. Binding free energies and individual energy terms of complexes starting from docked conformations (kcal/mol). The polar (ΔEpolar = ΔEele + ΔGele,sol) and non-polar (ΔEnon-polar = ΔEvwd + ΔGnpol,sol) contributions are shown. All the energies are averaged over 500 snapshots at time intervals of 100 ps from the last 50 ns-long MD simulations and are in kcal/mol (± standard error of the mean)