I have a .SDF file and I want to perform a hydrolysis reaction. In particular, I want to attack the nitrogen with no hydrogens attached in a cytosine ring. I don’t know what the products should be. In fact, I want to figure out the products. Is there a Node I can use to perform such a reaction?
I tried using RDKit One Component Reaction but it required a SMARTS string as a reaction query. The SMARTS documentation by Daylight was not very helpful. Does anyone know a better tut/documentation?
I tried writing a SMARTS string as [N&H0;R] which would filter out the nitrogen I want but I don’t know how to write the transformation part. How do I make it react with H2O? Or does Knime not allow a way for this?
Hi Cartilage,
I think you are looking into the deamination reaction. Here what happens with a cytosine during the hydrolysis https://en.wikipedia.org/wiki/Deamination
Here is the documentation on the Reaction SMARTS from RDKit https://www.rdkit.org/docs/RDKit_Book.html#reaction-smarts
You could start figuring out the correct reaction SMARTS by using the MarvinSketch node and drawing a reaction there. Don’t forget to change the output to “SMARTS cell” in the configuration dialog of the node. After you’ve executed the node render the output to String in the Output table. You would need to tune the output of the MarvinSketch node by hand to get the correct reaction SMARTS.
You could also look into the RDKit Chemical Transformation node. It takes a table of molecules and a table of reactions as inputs and
I hope it helps to get you started.
Best, Daria