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. 2014 Feb 4;53(7):1218–1227. doi: 10.1021/bi401582t

Figure 7.

Figure 7

Docking of DB1255 to d[(5′-CCATGATCT-3′)(5′-AGATCATGG-3′)] by using Autodock version 4.02. Two thiophene S atoms (yellow) form bifurcated hydrogen bonds with the G-NH in the minor groove (shown with a yellow dashed line). The lower amidine group forms H-bonds with the thymine (T) carbonyl of T4, which is at the 5′ side of G on the opposite strand), and to a deoxyribose oxygen of the DNA backbone (yellow dashed lines) on the same strand as G. The top amidine group is adjacent to the flanking 3′-T in cATGAt and forms an H-bond with the DNA backbone (yellow dashed line). The DNA backbone is shown as a stick model, colored by atom type (gray for carbon, red for oxygen, blue for nitrogen, and orange for phosphorus). The G5 base is displayed as a ball and stick and colored by atom type (cyan for carbon, white for hydrogen, and blue for nitrogen), and the ligand is displayed as a ball and stick also and colored by atom type (magenta for carbon, white for hydrogen, and blue for nitrogen).