[gmx-users] TZD Tautomers

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jan 14 06:12:32 CET 2011


Mark already indicated that this is not the proper place to post
questions like that. This forum is about gromacs, not about tautomers,
docking, and certainly not about MarvinSketch.



On Thu, Jan 13, 2011 at 10:26 PM, Nancy <nancy5villa at gmail.com> wrote:
> Hi All,
> I happened to find a published article where molecular docking simulations
> of TZDs against a novel protein is detailed:
> "Structure-based design of a thiazolidinedione which targets the
> mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb
> 1;20(3):819-23
> In this paper, the authors, using MarvinSketch v3.5.4, determined that the
> TZDs would exist predominantly in the enol form at pH 7.4, as opposed to the
> diketone form (see attached figure).  It appears that the article's tautomer
> prediction was based only on the pH prior to docking, and had nothing to do
> with ligand-protein interactions.
> Does anyone know if the diketone or enol, or perhaps a different tautomer,
> would be predominant at pH 7.4?
> Thanks in advance.
> Nancy
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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