Hi Paolo,
Thank you so much for your kind advice. Yes that works well for my compounds as
they are mostly analogs to GC373. Thanks again for your kind help!
Bests,
Amy
--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
he.1...@osu.edu
From: Paolo Tosco <paolo.tosco.m...@gmail.com>
Date: Tuesday, July 26, 2022 at 3:05 PM
To: He, Amy <he.1...@buckeyemail.osu.edu>
Cc: rdkit-discuss@lists.sourceforge.net <rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] How to draw peptides and let the backbone atoms
appear in the most extended form?
Hi Amy, the simplest way is probably to use Schroedinger's CoordGen to generate
coordinates:: from rdkit import Chem from rdkit.Chem.Draw import rdDepictor
rdDepictor.SetPreferCoordGen(True) peptide =
Chem.MolFromSmiles("CC(C)C[C@H](NC(=O)OCC1=CC=CC=C1)C(=O)N[C@@H](CC1CCNC1=O)C=O")
Hi Amy,
the simplest way is probably to use Schroedinger's CoordGen to generate
coordinates::
from rdkit import Chem
from rdkit.Chem.Draw import rdDepictor
rdDepictor.SetPreferCoordGen(True)
peptide =
Chem.MolFromSmiles("CC(C)C[C@H](NC(=O)OCC1=CC=CC=C1)C(=O)N[C@@H](CC1CCNC1=O)C=O")
rdDepictor.Compute2DCoords(peptide)
0
peptide
[cid:ii_l62jqp9b2]
Should this fail for other peptides, get in touch as there are alternative ways.
Cheers,
p.
On Tue, Jul 26, 2022 at 5:13 PM He, Amy
<he.1...@buckeyemail.osu.edu<mailto:he.1...@buckeyemail.osu.edu>> wrote:
Dear RDKit Experts,
I have a question about drawing peptidomimetic compounds. I wanted to draw the
peptides and let the backbone atoms appear in the most extended form. Please
see the following ChemDraw picture as an example for what I was trying to
achieve:
[cid:1823be2ebef847be2d22]
The molecule shown above is inhibitor
GC373<https://urldefense.com/v3/__https:/go.drugbank.com/drugs/DB15797__;!!KGKeukY!2ZFin_Fq-pYF9Ui-CxUV2gBcN_Ei7MpmB4sF7eca98u6EtGKnunDGjCKm5JB_w6J6GzPKgP7BazKPpPP7y6YCmoG_9pWszDQb2hjdf0$>.
The backbone atoms appear in the trans configuration. But this kind of “trans”
configuration is about the directionality of bonds around the C-N and C-C
single bonds, so I was unable to use the double bond configuration method (by
characters ‘\’ and ‘/’) to enforce this type of structure by SMILES… :’(
My RDKit structure from SMILES looks like this:
[VDgAn4AAAAASUVORK5CYII=]
My question is: Is it possible to adjust the drawing method so I can let the
backbone atoms lay out in the most extended form (the trans configuration as
shown in the ChemDraw picture)? Thank you for your time and kind advice in
advance.
Many Thanks,
Amy
--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
he.1...@osu.edu<mailto:he.1...@osu.edu>
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