Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites
Table 1
Relative contributions of multiple poses to predicted affinity.
Complex
Poses
DBF
EE
Spatial fit scoring
AcrB/minocycline
36
5 ± 2
2.5 ± 0.8
AcrB/acridine orange
68
14 ± 4
6.9 ± 1.2
AcrB/skatole
1494
57 ± 31
9.7 ± 5.7
AcrB/toluene
2429
661 ± 139
53.7 ± 10.1
OSBP/cholesterol
10
1.3 ± 0.3
1.1 ± 0.2
Cinnamomin/ergosterol
7
2.2 ± 1.1
1.7 ± 0.4
HSA/diazepam
5050
2298 ± 1703
435 ± 333
HSA/halothane
6897
4319 ± 1626
1630 ± 695
BAR/carazolol
3
1.8 ± 0.9
1.5 ± 0.4
Empirical scoring
AcrB/minocycline
52
8.5 ± 2.0
4.1 ± 1.7
AcrB/acridine orange
81
5.7 ± 3.1
3.3 ± 2.3
AcrB/toluene
1965
726 ± 67
107 ± 10
AcrB/skatole
1637
526 ± 58
76 ± 9
Abreviations: OSBP, oxysterol binding protein; HSA, human serum albumin; BAR, beta-adrenergic receptor. “Poses”, refers to number of possible () poses in binding region analyzed. Analyses performed in triplicate with runs of 100,000 MCMC steps.
