Figure 6.

(a) A snapshot of sertraline, where three rings, Ring A, B, and C are defined and Rings B and C are unified as Ring BC. Ligand’s orientation (red-colored arrow) is defined by an arrow pointing from the geometric center of Ring BC to that of Ring A. Panels (b) and (c) illustrate spatial patterns of $〈{\mathit{e}}^{\left(\text{sertraline}\right)}\left(\mathit{r}\right)〉$ in the cleft of mSin3B viewed from two different directions. The vectors $〈{\mathit{e}}^{\left(\text{sertraline}\right)}\left(\mathit{r}\right)〉$ are assigned to high-density regions of ${\rho }_{\mathit{CG}}^{\left(\text{sertraline}\right)}\left(\mathit{r}\right)>0.5{\rho }_0$ (${\rho }_0=0.001$) presented by gray contours. Red and black vectors are those with $\left|〈{\mathit{e}}^{\left(\text{sertraline}\right)}\left(\mathit{r}\right)〉\right|\ge 0.5$ and $\left|〈{\mathit{e}}^{\left(\text{sertraline}\right)}\left(\mathit{r}\right)〉\right|<0.5$, respectively. This figure also displays REST/NRSF bound to mSin3B (PDB ID: 2CZY), and the magenta-colored segment is the LIML sequence of REST/NRSF. Note that REST/NRSF is not involved in the current simulation. Labels H1,…, H4 are helices 1,…, 4 of mSin3B (PAH1 domain). (d) A snapshot of YN3, where “head” and “tail” are colored by purple and orange, respectively. Red-colored arrow is the YN3’s orientation pointing from the geometric center of tail to that of head. Panels (e) and (f) illustrate spatial patterns of $〈{\mathit{e}}^{\left(\text{YN}3\right)}\left(\mathit{r}\right)〉$. See captions for panels (b) and (c) for method to draw $〈{\mathit{e}}^{\left(\text{YN}3\right)}\left(\mathit{r}\right)〉$ from two different directions. (g) A snapshot of acitretin, where “head” and “tail” are colored by purple and orange, respectively. Red-colored arrow is the acitretin’s orientation pointing from the geometric center of tail to that of head. Panels (h) and (i) illustrate spatial patterns of $〈{\mathit{e}}^{\left(\text{acitretin}\right)}\left(\mathit{r}\right)〉$ from two different directions. See captions for panels (b) and (c) for method to draw $〈{\mathit{e}}^{\left(\text{acitretin}\right)}\left(\mathit{r}\right)〉$.