Overview of ChEMBL Database
Gareth Owen, ChEBI group, EMBL-EBI
Northwestern University
16 th October 2012
EBI is an Outstation of the European Molecular Biology Laboratory.

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What is ChEMBL?
• Open access database for drug discovery
• Freely available (searchable and downloadable)
• Content:
• 2D structures & calculated properties (logP, MW, Lipinski, etc.)
• Associated bioactivity data extracted from the primary medicinal chemistry journals such as J. Med. Chem.
• Deposited data from neglected disease screening (e.g. malaria)
• Subset of data from PubChem
• Covers ~30 years of compound synthesis and testing
• Annotated FDA-approved drugs
• Secure searching ( https://www.ebi.ac.uk/chembldb )

ChEMBL Database
• Content
ChEMBL14
Targets: 9,003
Compounds: 1,376,469
Activities: 10,129,256*
Publications: 46,133
* Includes:
~5,900,000 (PubChem)
~100,000 (Deposited malaria screening sets)
Assays are classified as:
• Binding measurements
• Functional assays
• ADME/toxicity data
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60% proteins
20% organisms
20% cell lines
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ChEMBL Assays –
Binding, Functional, ADMET
Binding Assays
• Assays which directly measure the binding of a compound to a particular target
• E.g., competition binding assays with a radioligand
• Various endpoints measured, but most commonly reported are:
• IC50 (half maximal inhibitory concentration)
• Ki (binding affinity)
• MIC (minimum inhibitory concentration)
• % Inhibition (of activity)

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Functional Assays
Whole organism assays
(e.g., anti-infectives/parasitics)
Disease-derived cell-line
(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)

ADMET Assays
• Assays measuring:
Absorption, Distribution, Metabolism, Excretion, Toxicity properties of compounds
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• Examples include:
• Half-life of compound in rats
• Tissue distribution of compound
• Levels of metabolites

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ChEMBL Targets:
Protein Protein complex Protein family Nucleic Acid e.g., PDE5 e.g., Nicotinic acetylcholine receptor e.g., Muscarinic receptors e.g., DNA
Cell Line Tissue Sub-cellular Fraction Organism e.g., HEK293 cells e.g., Nervous e.g., Mitochondria e.g., Drosophila

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Protein Targets
• Each protein target linked to a sequence in UniProt
• Information from UniProt used in ChEMBL to allow searching:
• Protein name/description
• Synonyms and gene names
• Organism (and NCBI Tax ID)
• Proteins in ChEMBL also classified according to family
(e.g., Receptor, Kinase, Protease, Transporter etc).
• Used for searching by target tree (Browse Targets)

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ChEMBL Compounds
• Chemical structures are stored as .mol files
• If the stereochemistry is known it is drawn as a specific enantiomer
• Tautomers of the same compound are treated as the same compound. The form shown is as in the paper
• Identifying unique compounds is done using standard Inchis
• Salts and parent molecules are grouped together for displaying bioactivity data although activity data is recorded against the specific salt

ChEMBL Home Page
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ChEMBL Main Search Page

Drug
Information
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Small molecule resources at the EBI
Clickable structure
Parent and Salt
Forms

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Click to display data

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ChEBI Link:

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This will take you back to ChEMBL

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ChemSpider Links:
The link works both ways. They link TO
ChemSpider and
FROM
ChemSpider.
They link on
Standard_Inchi

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Wikipedia Links:
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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Use Case 1 - Searching by Target
• What is known about chemical structures that bind to a specific protein (Adenosine A2a)?
• What is known about their potency/selectivity/ADMET
Properties
• Is there any protein structure data?

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Use Case 1 Searching by Target in ChEMBL
Choose Sources to include in search

Retrieving Bioactivity Data - Single Target
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Bioactivity data for target
Assay data for target
3D Structures
Display all bioactivity data for target
Click pie chart to retrieve particular end-points

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Select targets of interest
Filtering Bioactivities
Select required activity types and define cut-offs e.g Ki<100nM

Bioactivity Results
Compound structures
Activity values
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Assay details Target details References

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Selectivity Data
For example:
Can search ChEMBL for all data on compounds that have adenosine A2a Ki values <100nM

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ADMET Data
Summary of ChEMBL bioavailability data for compounds with A2a Ki values <100nM
Example of
Bioavailability data

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Use Case 2 – Searching by Structure
• What compounds contain a particular substructure?
• What is known about their bioactivities?
• Known drugs/clinical Trials

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Lists of Identifiers
Different sketchers
Types of synonyms:
• Research codes
• Trade names
• INN, USAN

Similarity and Substructure Searching
31 Display/Download Bioactivity Data

Filtering Data on Lipinski Properties etc
32 Display Bioactivities of subset

names
Bioactivities
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Structure

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Bioactivities
Properties
Cross-references
Clinical Trials

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Links to Other Resources

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Links to Other Resources
PDBe http://www.ebi.ac.uk/pdbe

Marketed Drugs
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Select set of interest
Export to Excel or
Export SDF

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Use Case 3 – Similar Targets
• 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 Search
• More precise method for identifying targets
• Input is a protein sequence of interest
• Uses BLAST* algorithm to perform pair-wise comparisons between input sequence and all proteins in the Target
Dictionary, to find most closely related matches
• Results are scored according to similarity to input sequence (determined by number of amino acids that are identical or have similar properties)
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*Altschul SF et al., J Mol Biol. 215(3), p403-10 (1990)

Use Case 3 – Similar Targets
Protein Sequence of
Interest e.g from UniProt http://www.uniprot.org
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Data on IRAK1,IRAK3 and
IRAK4 but not IRAK2

IRAK1, IRAK3 and IRAK4 data
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Identify sub-structure of interest
What other data available on compounds with this sub-structure?

Use Case 4 - Assay keyword search
• Some ChEMBL data (e.g., functional assays) may not be mapped against molecular targets
• May want to perform a more general search (e.g., for a disease process, animal model, cell type of interest)
• Examples:
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What compounds have been tested in disease models (cholesterol lowering)?
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What data is available for brain penetration (brain to plasma ratio)?
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Assay Search for “Cholesterol Lowering”

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Assay Search for “Brain to Plasma”

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Accessing ChEMBL Data

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Useful Links
ChEMBL Blog: http://chembl.blogspot.com
If you would like help: chembl-help@ebi.ac.uk
For ChEMBL news and data releases subscribe to: http://listserver.ebi.ac.uk/mailman/listinfo/chembl-announce

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Acknowledgements
ChEMBL Group
John Overington
Anne Hersey
Anna Gaulton
Mark Davies
Jon Chambers
Louisa Bellis
Kazuyoshi Ikeda
Patricia Bento
Shaun McGlinchey
Yvonne Light
Felix Krueger
Ben Stauch
Ruth Akhtar
Francis Atkinson
Rita Santos
EMBL-EBI
Samuel Kerrien, Sandra Orchard, Bruno
Aranda, Rafael Jimenez, Reactome,
UniProt and ChEBI teams
Collaborators
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

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Exercises!