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Sequence similarity searches in ChEMBL


The ChEMBL database contains bioactivity data that links compounds to their biological targets. Most ChEMBL targets are proteins (~ 70% in version 27) and these are mapped to their UniProt accessions. On the ChEMBL interface, searches can be performed with either protein names or accessions...but did you know that protein similarity searches are also possible?

Here’s an example using human Phospholipase DDHD2, a target not found in ChEMBL.

    1.     On the ChEMBL interface, click 'Enter a Sequence:

    2.     Input the FASTA sequence corresponding to human Phospholipase DDHD2 and click 'Search in ChEMBL':

 3.    Review the BLAST results, select targets of interest and browse bioactivity data:

The BLAST search identifies the mouse Phospholipase DDHD2 homologue alongside a small number of bioactivity data points and active compounds.

ChEMBL's sequence search feature is currently only available through the interface. However, sequence data for protein targets is available in the database download and can be found in the component_sequences table.


Questions? Please get in touch on the Helpdesk or have a look through our training materials and FAQs.


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