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Cambridge MedChem Consulting

ChEMBL 33 released

The latest update to ChEMBL has been released.

This fresh release comes with a few new data soures and also some new features: we added bioactivity data for understudied SLC targets from the RESOLUTE project and included a flag for Natural Products and for Chemical Probes. An annotation for the ACTIONTYPE of a measurement was included for approx. 270 K bioactivities. We also time-stamped every document in ChEMBL with their CREATIONDATE!

This version of the database, prepared on 31/05/2023 contains:

    2,399,743 compounds (of which 2,372,674 have mol files)
    3,051,613 compound records (non-unique compounds)
  20,334,684 activities
    1,610,596 assays
         15,398 targets
         88,630 documents

Full details are here

ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.

ChEMBL 32 is released!

The fantastic resource ChEMBL has been updated. ChEMBL 32 contains

  • 2,354,965 compounds (of which 2,327,928 have mol files)
  • 2,995,433 compound records (non-unique compounds)
  • 20,038,828 activities
  • 1,536,903 assays
  • 15,139 targets
  • 86,364 documents

More details are here

Data can be downloaded from the ChEMBL FTP site.

ChEMBL 31 is released

The latest release of the absolutely invaluable ChEMBL database is available.


This version of the database, prepared on 12/07/2022 contains:

    2,967,627 compound records
    2,331,700 compounds (of which 2,304,875 have mol files)
    19,780,369 activities
    1,498,681 assays
    15,072 targets
    85,431 documents

Available from the downloads page

ChEMBL 28 has been released.

I see that a new version of ChEMBL has been released. Chembl 28

  • 2,680,904 compound records
  • 2,086,898 compounds (of which 2,066,376 have mol files)
  • 17,276,334 activities
  • 1,358,549 assays
  • 14,347 targets
  • 80,480 documents


ChEMBL 26 Released

The latest release of the essential molecule bioactivity dataset has just been announced.

ChEMBL 26 contains

  • 2,425,876 compound records
  • 1,950,765 compounds (of which 1,940,733 have mol files)
  • 15,996,368 activities
  • 1,221,311 assays
  • 13,377 targets
  • 76,076 documents

A couple of notes

We are now using RDKit for almost all of our compound-related processing. For the first time in ChEMBL26, this will include compound standardization, salt-stripping, generation of canonical smiles, structural alerts, image depiction, substructure searches and similarity searches (via FPSim2: Therefore, all molecules have been reprocessed and you may notice some differences in molfiles, smiles and structure search results compared with previous releases. The ChEMBL structure curation pipeline has been released as an open source package:, and incorporated into our Beaker web services (see below). More information can be found here:

We are also now using ChemAxon tools to calculate most acidic and basic pKa, logP and logD (pH 7.4) predictions, rather than ACDLabs software. These properties have therefore been recalculated and renamed in the database.

The release notes contain more details and the database can be downloaded from the ChEMBL FTP site.

The Polypharmacology Browser PPB2

Off-target activity is often ignored and might only be uncovered relatively late in the drug discovery program. Whilst broad spectrum screening is available it can be rather expensive. Predicting potential off-target activities is an attractive approach and this paper describes the development of a prediction tool using nearest neighbours combined with machine learning.

The Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning DOI

To build PPB2 we collected a bioactivity dataset of all compounds having at least IC50 < 10 uM on a single protein target in ChEMBL22 considering only high confidence data points as annotated in ChEMBL and only targets for which at least 10 compounds were documented

You can try it out here PPB2., depending on the model chosen the results are calculated in a couple of minutes, but don't post your proprietary molecules. Typical results are shown below, clicking on the green "Show NN" button shows the most similar structures.