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. Author manuscript; available in PMC: 2008 Oct 28.
Published in final edited form as: Chem Res Toxicol. 2008 Jun 12;21(7):1457–1467. doi: 10.1021/tx800102e

Figure 4.

Figure 4

Examples of PXR non-activator and PXR activator compounds in the test set that are structurally similar. Red dashed circles highlight likely important structural features that may contribute to activity. Corresponding PXR activator compounds (that had correctly predicted classifications) were docked in the PXR structure (1NRL) with FlexX (as described in the Materials and Methods). Carbamazepine (circled group), loratadine (circled group) and nabumetone (C=O group next to circled group) are predicted to form hydrogen bonding interactions with the side chain NH of Gln-285, additionally the methyl group in nabumetone may interact with the Phe288. Naloxone is predicted to form a H-bond with the side chain C=O and His407 and the ethylene group may also have a hydrophobic interaction with the Phe288. Oxcarbazepine docks differently to Carbamazepine and may also form a H-bond between the side chain C=O and His407. The hydrogen bonding interactions are shown as a red dotted line. The amino acid residues are shown in the stick mode whereas the PXR activators are shown in the ball and stick mode (purple). The 3D images were created using Chimera.(77)