<p>The easiest solution to the problem of mapping chemical compounds to protein IDs is to use the ChEMBL compound ID to UniProt <a href="ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_24_1/chembl_uniprot_mapping.txt" rel="nofollow noreferrer">mapping</a>.</p>

<p>Doing this with PubChem is not so straight forward in part because its downloadable data format is a hideous obfuscated and badly documented mess split over multiple compressed files which in turn contain multiple compressed files...... For a publicly funded project they should really do better.</p>

CC BY-SA 4.0
2018-07-24T14:40:15.183Z
2018-07-24T14:40:15.183Z
Matt Bashton
<p>I want to get all Pubchem Chemical compounds (CID) that interact with a given UniProt target. I have a list of UniProt targets and I need to study the relationship between these targets and chemical compounds.</p>

<p>Thanks</p>

<uniprot><interactions>
How to get all chemical compounds that interact with a given protein target?
# How to get all chemical compounds that interact with a given protein target?

(Asked by: username_0 on 2018-07-23)

I want to get all Pubchem Chemical compounds (CID) that interact with a given UniProt target. I have a list of UniProt targets and I need to study the relationship between these targets and chemical compounds.

Thanks

**Tags:** uniprot, interactions

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## 1 answers

### Answer by username_1 on 2018-07-24. Score: 0 | Accepted answer

The easiest solution to the problem of mapping chemical compounds to protein IDs is to use the ChEMBL compound ID to UniProt [mapping](ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_24_1/chembl_uniprot_mapping.txt).

Doing this with PubChem is not so straight forward in part because its downloadable data format is a hideous obfuscated and badly documented mess split over multiple compressed files which in turn contain multiple compressed files...... For a publicly funded project they should really do better.


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