PubChem CID data retrieval
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5.8 years ago

Is there a way to retrieve all the pubchem CIDs for a given Uniprot ID from PubChem?

Uniprot PubChem CID FTP • 4.3k views
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5.6 years ago

This question could use some clarification as it is not clear what you are trying to achieve. There will not be anything like a 1-to-1 relationship between pubchem CIDs (which refer to chemical compounds) and Uniprot IDs (which refer to protein structures).

Are you interested in interactions between drugs (often chemicals) and proteins (encoded by gene loci)? Or are you interested in the small subset of proteins that are themselves used as drugs perhaps? These might be entered in PubChem as substances instead of compounds. Another option might be Chembl which does have a concept of uniprot to compound mapping.

ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_21/chembl_uniprot_mapping.txt

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In addition to ChEMBL, having a look at Open Targets may be useful. If you've got protein IDs, for example, you can get gene, variation, pathways associated with a drug target (i.e. gene product). You can search for a given protein (e.g. A4D1T4) and get the target profile (BRAF) and associated diseases with BRAF

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chembl_uniprot_mapping.txt have only chembl id not pubchem CID! Sir, How can I get pubchem CID from chembl id ?

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