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. Author manuscript; available in PMC: 2015 Oct 30.
Published in final edited form as: Eur J Med Chem. 2014 Sep 6;86:528–541. doi: 10.1016/j.ejmech.2014.09.009

Figure 7.

Figure 7

(a) The dimer interactions from the X-ray crystal structure (pdb: 3RQD). (b) superimposition of the X-ray crystal configuration (white ribbon) with the final structure from the molecular dynamics simulation (blue ribbon). Largazole thiols from X-ray (yellow) and simulation (red) are shown in the ball-and-stick and surface representations; (c) Largazole thiol (ball-and-stick) form MD simulation shown with the D101 interaction with N14; (d) C7-epimer docked at the largazole binding site of HDAC showing the steric contacts with the backbone atoms of the loop containing D101. Moving this loop away from the C7-epimer results in the broken hydrogen bond between D101 and N14.