ADL: Unsuccesful redocking

Leo Juhlin leojuhlin at
Mon Apr 13 05:51:24 PDT 2020

I tried to redock a ligand into a known crystal structure. Even though I
used the same protein as from the crystallized structure I still get the
highest ranked pose with an carboxy group pointing in the opposite
direction in comparison the crystallized ligand, as can be seen in the
linked picture below. I´ve run the docking multiple times both in vina and
autodock4 but still get this pose.

It doesn´t make sense to get this pose since the carboxy group of the true
ligand pose is hydrogen-bonding with a positively charged lysine side chain

Could anyone give me some advice why I won´t get the right pose?

Best regards, Leo

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