## 3 Results
### CAR Protein (Androstan Receptor)  
Only a single PDB structure is currently available in the PDB database for the constitutive androstane receptor (CAR). This is the 1 XNX entry describing the structure obtained from _Mus musculus_ by X-ray diffraction with a resolution of 2.9 A (Figure 7). The sequence identity with the human protein is very high (74%), and the sequence similarity is close to 85%. This suggests that 1 XNX can be used with reasonable confidence to explore the potential binding of ceruchinol to this target protein.  
The 1 XNX structure comes with a unique ligand called 16,17-androstene-3-ol (ID: ATE), which is similar to ceruchinol (Figure 8). Before running the docking of ceruchinol, we  
Figure 7: Structure of the constitutive androstane receptor with its unique ligand 16,17-androstene-3-ol (shown in orange).  
tested the method using ATE as a control in a redocking calculation. The result calculation indicates that the simulated pose of ATE does not coincide exactly with that of the X-ray structure, but the predicted pose is still acceptable since the positional root-mean-square deviation (RMSD) of the re-docked ligand (RMSD = 0.90 A) is lower than 2 A, as noted in Figure 9. The slight displacement observed between predicted and X-ray poses is most likely due to the absence of a water molecule bridging the hydroxyl group to the His [213] imidazole ring (note that water molecules were eliminated before the docking calculation and hence the docked ligand tends to form a direct interaction with His [213]). The total energy (E\({}_{\text{tot}}\)) is 2.3 kcal/mol, the interaction energy (E\({}_{\text{I}}\)) is \(-\)31.5 kcal/mol, and the docking score (S) is \(-\)8.8 kcal/mol.  
Docking of ceruchinol produced two different poses with slightly different total and interaction energies but very similar docking scores (Table 2). As shown in Figure 9, the ligand is surrounded by non-polar amino acids (e.g., Phe [171], Phe [227], and Ile [174]) which stabilise the ligand via hydrophobic interactions. In pose 1, the hydroxyl group is coordinated to Lys [235] and is further stabilised via H-bond interaction. In pose 2, the nearest polar residue (Asn [175]) is 5.0 A away from the -OH group, but this interaction could be stabilized through a water-mediated interaction, which could be facilitated if one assumes some degree of structural plasticity in the side chains that shape the binding pocket. Considering this, the two poses are retained, and they suggest that the ligand could bind the target protein.  
\begin{table}
\begin{tabular}{l c c c} \hline \hline  & **Total Energy (kcal/mol)** & \
\begin{tabular}{c} **Interaction Energy** \\ **(kcal/mol)** \\ \end{tabular} &
\begin{tabular}{c} **Docking Score** \\ **(kcal/mol)** \\ \end{tabular} \\ \hline Pose 1 & 12.4 & \(-\)30.1 & \(-\)10.2 \\ \hline Pose 2 & 15.7 & \(-\)27.0 & \(-\)10.1 \\ \hline \hline \end{tabular}
\end{table}
Table 2: Total energy, interaction energy and docking score for the two poses of ceruchinol docked to the constitutive androstane receptor.  
Figure 8: Chemical structure of (**left**) ceruchinol and (**right**) 16,17-androstene-3-ol (ID: ATE).  
Figure 9: Result of the control docking simulation. The co-crystallized ligand is shown in orange and the re-docked ligand is shown in yellow.