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. 2019 Oct 21;11(19):2491–2504. doi: 10.4155/fmc-2019-0181

Figure 4. . Binding mode of methylated thiophenes in subsite 2.

Figure 4. 

(A) Crystal structure of the Y220C-PK9328 complex (Protein Data Bank [PDB] ID 6GGF). Cross-section of the binding pocket. The Y220C mutant protein is shown as a surface representation. Selected side chains and the ligand are shown as stick models. 2Fo–Fc electron density for the ligand is shown in blue at a contour level of 1.5 σ. (B) Structure of Y220C-PK9328 (green) superimposed onto Y220C-PK9318 (gray; PDB ID 6GGB). Shown are Cα traces and selected side chains plus ligands as stick models. (C) Superposition of the binding modes of PK9328 (green stick model) and PK9318 (magenta stick model) shown in a different orientation, highlighting the rotation of the thiophene moiety upon methylation. The protein chain of the Y220C-PK9328 complex is shown in gray, with selected residues in the binding pocket displayed as stick models. (D) Structure of Y220C-PK9327 (pink; PDB ID 6GGE) superimposed onto Y220C-PK9318 (gray). Shown are Cα traces and selected side chains plus ligands as stick models. In all four panels, chain B of the asymmetric unit is shown.