[gmx-users] Pioglitazone Tautomers

[Tsjerk Wassenaar]

Hi Nancy,

This isn't really a Gromacs related question, and it would be better
fit on some chemistry forum. Anyway, whatever answer may come to you,
mind that you're interested in the receptor bound form, which may not
be what you'll find to be the dominant form. It will depend on the
hydrogen bonded network in the pocket. Also, the proton is also
probably quite acidic, as the negative charge can delocalize nicely
over the ring and the carbonyls, so make sure you're looking at the
protonation state too.

Hope it helps,

Tsjerk

On Mon, Jan 10, 2011 at 12:11 AM, Nancy <nancy5villa at gmail.com> wrote:
> Hi All,
>
> I am performing molecular docking and molecular dynamics simulations of the
> thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein
> (PDB ID: 1ZGY).  The thiazolidinedione ring can exist in numerous different
> tautomeric states; I have attached a figure depicting several of them.
> Which tautomer would be dominant at the physiological pH of ~7.0?
>
> Also, are there any software programs that can predict which tautomer would
> be correct?
>
> 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