|
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
|
- 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.
