Objective

To use the right click options in the chemical search window to add additional search criteria and find ways to distinguish Celebrex from Rofecoxib.

Instructions

1. Load the celebrex50.sdf file into ICM (File/Open). This file is provided in the ICM distribution. Add Rofecoxib to the celebrex50.sdf file as described in the chemical-edit tutorial.
2. Chemistry/Chemical Search
3. The ICM Molecular Editor and another menu for query search (on the right) will be displayed.
4. If a molecule is already displayed in the editor you can delete it by Edit/Select All to delete
5. Follow the search instructions described in the previous example with the following chemical search substructures:

Celebrex contains halogen atoms and Rofecoxib does not - therefore one way to distinguish the two would be a simple filter as shown below.

One of the key features between Celebrex and Rofecoxib is a benzene ring connected to a five-membered ring. The difference is that in celebrex the connection point is with a nitrogen atom and in Rofecoxib the connection point is with a carbon atom. Therefore to retrieve both Celebrex and Rofecoxib in the results table you would need to right click and select Element/Any (*) and select Ring Size 5 (r5) or to retrieve only one you would need to specify nitrogen or carbon at the connection point.

You can also perform the same query using Ring Membership (R1) or Attachment Point.

Manual References (Web Links)

Chemical Similarity Searching