[Dock-fans] Fixing protonation state

John J. Irwin jji at cgl.ucsf.edu
Thu Nov 1 10:50:28 PDT 2007

Hi Asdrubal

That molecule has more rotatable bonds (13 in a row, 17 total, + limited
sampling on the 2 amides) than I feel comfortable with. It also has
molecular weight > 600. These are two reason why the ZINC upload server
just won't take it. I have to draw the line somewhere, and I regret to
say you have hit it.

I would be skeptical of anyone who docks a molecule having 17 (or even
13) rotatable bonds and gets the crystallographic pose within 2A rmsd.
Actually, my skepticism starts at around 8 rotatable bonds, but I keep
it mostly to myself till we get past 12. ;-)

Almost for sure, you are trying to dock into two distinct pockets, and
the long aliphatic chain is a linker between them. My suggestion is
therefore to dock each end separately. Shoot for something with 7
rotatable bonds, even a bit less if you can. Then you can model in the
rest of the linker between them.

Good luck, and sorry to disappoint.


burgosgu at ualberta.ca wrote:
> Hi everybody,
> I need to have a compound correctly protonated to dock it. I tried to  
> use the resource of
> "upload sets" of ZINC, but it seems that it does not have the required  
> charactersitics of
> bioavailability and non-toxicity, because it gives me no output as it  
> did with other
> compounds.
> The smile for this compound is:
> Any suggestions??
> Asdrubal
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans

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