Overview of ChEMBL Database. Gareth Owen, ChEBI group, EMBL-EBI Northwestern University 16 th October 2012. What is ChEMBL?. Open access database for drug discovery Freely available (searchable and downloadable) Content:
Gareth Owen, ChEBI group, EMBL-EBI
16th October 2012
20% cell lines
~100,000 (Deposited malaria screening sets)
Whole organism assays
(e.g., human ovarian cancer cell line cytotoxicity)
Tissue or cell-based disease model
(e.g., glucose uptake by adipocytes)
Tissue or cell-based assay for target effect
(e.g., contraction of guinea-pig ileum)
Cell-based assay over-expressing target
(e.g., GPCR calcium mobilisation)
Protein Protein complex Protein family Nucleic Acid
e.g., Muscarinic receptors
e.g., Nicotinic acetylcholine receptor
Cell Line TissueSub-cellular Fraction Organism
e.g., HEK293 cells
Parent and Salt Forms
Small molecule resources at the EBI
The link works both ways. They link TO ChemSpider and FROM ChemSpider.
They link on Standard_Inchi
We also have links with Wikipedia. These also use the Standard_Inchi as the common identifier. These links will link to the Compound Report Card in ChEMBL.
The links are added by a ChemoBot and can be updated with each release, if required.
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Bioactivity data for target
Display all bioactivity data for target
Assay data for target
Click pie chart to retrieve particular end-points
Select targets of interest
Select required activity types and define cut-offs e.g Ki<100nM
For example:Can search ChEMBL for all data on compounds that have adenosine A2a Ki values <100nM
Summary of ChEMBL bioavailability data for compounds with A2a Ki values <100nM
Example of Bioavailability data
What compounds contain a particular substructure?
What is known about their bioactivities?
Known drugs/clinical Trials
Lists of Identifiers
Display/Download Bioactivity Data
Display Bioactivities of subset
PDBe - http://www.ebi.ac.uk/pdbe
Select set of interest
Export to Excel or
Are there any available data on compounds that bind to proteins similar to IRAK2?
For these compounds what bioactivity data is there on compounds with related sub-structures?
Is there any crystal structure data on these proteins?
Protein Sequence of Interest e.gfrom UniProt
Data on IRAK1,IRAK3 and IRAK4 but not IRAK2
Identify sub-structure of interest
What other data available on compounds with this sub-structure?
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Samuel Kerrien, Sandra Orchard, Bruno Aranda, Rafael Jimenez, Reactome, UniProt and ChEBI teams
Imperial Cancer Research, University of Dundee, University of Cambridge, Sanger Centre, University of Maryland, NCBI, TDR, IUPHAR, Bayer-Schering, Pfizer, GSK, Schering-Plough, MMV, Novartis, St Jude Children’s Research Hospital
Former Inpharmatica colleagues