Submission Details
Molecule(s):
O=c1c(NCCN2CCNCC2)c(N(Cc2ccccn2)Cc2ccccn2)c1=O
Design Rationale:
This compound, already published (please see https://doi.org/10.1039/C9DT01434A) and called simply by "L" or "sdp", was designed by me and my PhD advisor for a different purpose. However, when I was looking to the pockets available in this S protein, which seem very prone to allow binding of small molecules, I immediately thought of this sdp compound. It is a molecule very predisposed to establish hydrogen bonds and pi-pi interactions. Unfortunately, at the present, I'm no expert in computational studies, but many of you are, so please if you can, include this molecule in your calculations. Furthermore, the synthetic pathway is rather simple, only two steps to the final compound (see the article), and it is water soluble, and all the pK's in strictly aqueous solution were determined. The log K values are: 8.81, 3.76, 2.80, 2.24, meaning that the most dominant species is HL+ between pH ~ 4 and ~ 9.
Other Notes:
We do not have the single crystal X-ray structure of sdp, but we have the structure of the product from the first step of the synthetic pathway: http://www.rsc.org/suppdata/c9/dt/c9dt01434a/c9dt01434a2.cif Please note that I did not use any fragment as inspiration, but in order to submit this form it is mandatory that I select one. I've selected the 1st.