The substructure search in the CSD web interface uses the Elemental sketcher from Dotmatics (https://www.dotmatics.com/) to create a query in SMARTS format that is then used to search the CSD. This SMARTS format (SMiles ARbitrary Target Specification) is simply a language for describing substructures in molecules that can be represented as a simple string of ASCII characters. Users do not need to understand SMARTS to use this search interface, but you can see what the SMARTS pattern for your sketched substructure looks like by clicking on the Advanced button underneath the sketcher and then clicking Import From Editor. If you would like to learn more about SMARTS or visualise SMARTS patterns, the web application SMARTSviewer by the University of Hamburg is an excellent reference.
The alternative CSD Sketcher that is under development currently uses a similar SMARTS query format.