SENSAAS-Bioisostere

Tutorial 3: Scaffold-hopping of type 4 to optimize inhibitors of EP300

Download Molecule (+)-3: 7vhy_F_6QI.sdf extracted from the PDB complex 7VHY
Download the bioisostere 6TI.sdf (PDB complex available at 7VHZ)

Link to the original publication

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NEXT (10/10) - Results

Inputs:
Reference 7vhy_F_6QI.sdf
Fragment to replace is number 3 in lib1.sdf
Database pdb2

Results
In this tutorial, results show that the molecule number 28 in ordered-bioisosteres-pdb2.sdf corresponds to the bioisostere Molecule 7 in the publication

Download best aligned bioisosteres ordered-bioisosteres-pdb2.sdf (373) and scores ordered-bioisosteres-pdb2-score.txt (more information on scores).
To visualize superimposition results: 3Dviewer

You can install and use DataWarrior (free software) to read the SDF file content as a table (available for Windows/Linux/MacOS-X)
Note: it has been observed that the minimization of some molecular structures is not sufficient with the standard process (RDKit, MMFF94 force field, 2000 Minimization cycles). This can sometimes cause some structure distortion).

Run completed

To visualize results, you can use this webtool 3Dviewer and click to display superimposed bioisosteres