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Table 5 Comparison of binding energy of molecular docking Vina, LeDock, and DS

From: Study on the potential active components and molecular mechanism of Xiao Huoluo Pills in the treatment of cartilage degeneration of knee osteoarthritis based on bioinformatics analysis and molecular docking technology

Compound

Structure

Target (Ligand)

Binding energy

Vina (kcal mol−1)

LeDock (kcal mol−1)

DS (LibDockScore)

Quercetin

VEGFA(5T89)

− 6.00

− 5.09

–

CCND1(2W96)

− 6.30

− 5.59

90.3571

MYC(5I42)

− 8.00

− 7.70

–

JUN(3V3V)

− 8.80

− 6.00

99.4514

MMP9(6ESM)

− 9.90

− 6.86

145.044

MMP2(4WK7)

− 9.50

− 6.82

138.262

Stigmasterol

VEGFA(5T89)

− 4.90

− 4.08

–

CCND1(2W96)

− 6.50

− 4.00

87.8871

MYC(5I42)

− 6.40

− 5.38

–

JUN(3V3V)

− 7.20

− 4.86

107.282

MMP9(6ESM)

− 8.50

− 5.12

–

MMP2(4WK7)

− 5.80

− 4.98

117.641

Beta− sitosterol

VEGFA(5T89)

− 5.70

− 4.25

–

CCND1(2W96)

− 6.40

− 4.27

–

MYC(5I42)

− 6.30

− 5.53

–

JUN(3V3V)

− 9.50

− 5.23

109.886

MMP9(6ESM)

− 8.80

− 5.57

–

MMP2(4WK7)

− 7.40

− 5.14

124.419

Izoteolin

VEGFA(5T89)

− 5.50

− 4.02

–

CCND1(2W96)

− 5.70

− 4.70

–

MYC(5I42)

− 6.10

− 5.95

–

JUN(3V3V)

− 8.80

− 5.89

96.172

MMP9(6ESM)

− 7.70

− 5.27

117.762

MMP2(4WK7)

− 8.30

− 5.86

118.482

Ellagic acid

VEGFA(5T89)

− 6.10

− 4.38

–

CCND1(2W96)

− 6.30

− 4.92

–

MYC(5I42)

− 6.30

− 6.44

–

JUN(3V3V)

− 9.50

− 6.40

100.529

MMP9(6ESM)

− 7.70

− 5.47

132.727

MMP2(4WK7)

− 8.60

− 5.80

120.031