ChEMBL Resources

The SARfaris: GPCR, Kinase, ADME

Tuesday, 3 February 2015

ChEMBL 20 Released

We are pleased to announce the release of ChEMBL_20. This version of the database was prepared on 14th January 2015 and contains:
  • 1,715,135 compound records
  • 1,463,270 compounds (of which 1,456,020 have mol files)
  • 13,520,737 activities
  • 1,148,942 assays
  • 10,774 targets
  • 59,610 source documents
You can query the ChEMBL 20 data online via the ChEMBL Interface and you can also download the data from the ChEMBL ftpsite. Please see ChEMBL_20 release notes for full details of all changes in this release.


Changes since the last release

In addition to the regular updates to the Scientific Literature, PubChem, FDA Orange Book and USP Dictionary of USAN and INN Investigational Drug Names this release of ChEMBL also includes the following new datasets:


 AstraZeneca in-vitro DMPK and physicochemical properties

AstraZeneca have provided  experimental data on a set of publicly disclosed compounds in the following ADMET related assays: pKa, lipophilicity (LogD7.4), aqueous solubility, plasma protein binding (human, rat, dog, mouse and guinea pig), intrinsic clearance (human liver microsomes, human and rat hepatocytes). For more details please refer to the AstraZeneca dataset document report page. Many thanks to Mark Wenlock and Nicholas Tomkinson for providing this data set.


MMV Malaria Box

Twelve new depositions from groups around the world screening the MMV Malaria Box have been loaded into ChEMBL 20. The groups include University of Yaoundé, University of Washington, University of Milan, Griffith University, Stanford University, National Cancer Institute, Weill Cornell Medical College, University Hospital Essen, Obihiro University of Agriculture and Veterinary Medicine, University of Toronto, Imperial College and Medicines for Malaria Venture.


HELM Notation

We have worked with members of the Pistoia Alliance to develop an implementation of the HELM standard for biotherapeutics and applied this to ChEMBL peptides (see associated press release). HELM notation has been generated for just under 19K peptides that were previously associated with Mol files in the database and that contain at least three amino acids. Our monomer library (containing the definitions/names of each of the amino-acids used) is available on the FTP site, and can be used by others to generate their own HELM notation. Abarelix is an example of a ChEMBL molecule that with HELM notation, which is now available on the compound report card page:


 Structural Alerts

We have compiled a number of sets of publicly-available structural alerts where SMARTS were readily available and useable; these include Pfizer LINT filters, Glaxo Wellcome Hard Filters, Bristol-Myers Squibb HTS Deck Filters, NIH MLSMR Excluded Functionality Filters, University of Dundee NTD Screening Library Filters and Pan Assay Interference Compounds (PAINS) Filters. These sets of filters aim to identify compounds that could be problematic in a drug-discovery setting for various different reasons (e.g., substructural/functional group features that might be associated with toxicity or instability in in vivo info settings, compounds that might interfere with assays and for example, appear to be 'frequent hitters' in HTS).

It should be noted however that some alerts/alert sets are more permissive than others and may flag a large number of compounds. Results should therefore be interpreted with care, depending on the use-case, and not treated as a blanket filter (e.g., around 50% of approved drugs have 1 or more alerts from these pooled sets). The compound report card page now provides a summary count of the number of structural alerts hits picked up by a given molecule:

The link in the Structural Alert summary section takes the user to the Structural Alert Details page:


Pesticide MoA classification

For molecules in ChEMBL that are known pesticides, we have included the mode of action classification assigned by the Fungicide Resistance Action Committee (FRAC), Herbicide Resistance Action Committee (HRAC) and Insecticide Resistance Action Committee (IRAC). These classification schemes group pesticides both by their mode of action and chemical class. The classifications can be seen in the Compound Cross References section of the Compound Report Card pages. Thiabendazole is an example of a ChEMBL molecule which has been assigned a FRAC mode of action classification:

This complements the ATC classification used for human drugs.


Cells, Cell Lines and LINCS integration

We now provide CHEMBL IDs for all cell lines stored in the ChEMBL database and we have also provided cross references to the LINCS project. To help users access the cell line data more easily we have setup a new cell search end point on the ChEMBL Interface, an example search output is displayed below:

A new Cell Report Card page has also been created:

EBI Complex Portal

For protein complex targets (e.g., CHEMBL2093869) we now have cross-references to the EMBL-EBI Complex Portal, a new resource providing manually curated information for stable protein complexes from key model organisms (see DOI: 10.1093/nar/gku975 for more details).

MedChemComm content

As mentioned in the previous release, the visionary staff at the RSC have donated free access of their MedChemComm journal for abstraction into ChEMBL. This for us is a significant event, a commercial publisher giving access to their content, and assisting with it's extraction and integration into ChEMBL. So, here's a big thanks to them for this. Of course, this now sets us the challenge of selling this idea to other publishers!

RDF Update

The EBI-RDF Platform has also been updated with the ChEMBL 20 RDF. You can run the SPARQL queries online or download the ChEMBL 20 RDF files from the ftpsite.

We recommend you review the ChEMBL_20 release notes for a comprehensive overview of all updates and changes in ChEMBL 20 and as always, we greatly appreciate to reporting of any omissions or errors.

Keep an eye on the ChEMBL twitter and blog accounts for news on forthcoming myChEMBL and UniChem updates.

The ChEMBL Team

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