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Table 1 Ensemble analysis of the binding sites of protein-protein interaction inhibitors

From: Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets

Protein

Binding site size (atoms)

Method

Percentage of site identified as pocket-lining

   

apo structure

Provar Score > 0.75

Provar Score > 0.25

  

PASS

38

21

64

Bcl-X L

56

LIGSITE

73

69

91

  

fpocket

52

36

89

  

PASS

46

15

50

MDM2

48

LIGSITE

52

38

77

  

fpocket

38

6

45

  

PASS

29

26

69

XiapBir3

42

LIGSITE

67

52

98

  

fpocket

31

24

83

  

PASS

25

16

54

XiapBir3

63

LIGSITE

57

44

87

  

fpocket

30

19

74

  

PASS

70

35

75

ZipA

20

LIGSITE

35

5

60

  

fpocket

0

15

15

  

PASS

46

23

54

HPVE2

97

LIGSITE

44

26

56

  

fpocket

33

2

53

  

PASS

38

7

58

IL2

60

LIGSITE

22

22

62

  

fpocket

0

2

2

  

PASS

53

53

68

HIV-1 Integrase

19

LIGSITE

37

16

47

  

fpocket

68

5

58

  

PASS

6

0

29

TNFa

34

LIGSITE

3

0

44

  

fpocket

0

0

3

  

PASS

0

0

69

TNFR1a

16

LIGSITE

50

38

100

  

fpocket

0

0

69

  

PASS

62

30

57

MDM4

81

LIGSITE

44

31

68

  

fpocket

38

0

42

  

PASS

38.5

20.5

59

Mean Values

49

LIGSITE

49

31

72

  

fpocket

37.5

8.5

48

  1. Provar analysis of a tCONCOORD generated ensemble of 250 structures of the apo form of each of the 11 proteins in the 2P2I database identifies a greater proportion of the known binding site atoms as pocket-lining than analysis of the crystallographic structure alone. The proportion of inhibitor binding-site atoms found to be persistently or variably lining pockets (defined as pocket-lining in at least 25% of conformers) is significantly greater than for the protein as a whole in 21/33cases. (An italic number in the final column indicates the minority of cases in which the proportion is not significant at the p < 0.05 level). Further details of the structures are given in Table 4.