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ChEMBL 36 is out!

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📊 Database Scale

🆕 New Data Sources

  • Src_ID 72 – Chemical Probe data from Scientific Literature

    • NLP and manual extraction from probe-related publications.

    • Includes phenotype/disease context, mapped to EFO ontology.

    • Stored in assay_parameters.

🔄 Updated Data Sources

AI-driven Structure-enabled Antiviral Platform (ASAP)
Active Ingredient of a Prodrug
BindingDB Patent Bioactivity Data
British National Formulary (BNF)
Clinical Candidate Compounds
EMBL Heidelberg Gut Microbiome–host Interactions
EUbOPEN Chemogenomic Library
EUbOPEN Chemogenomic Library Literature Data
European Medicines Agency (EMA)
FDA Novel Drugs and Biotherapeutics
FDA Orange Book Drugs
International Nonproprietary Names (INN) for Pharmaceutical Substances
SGC Frankfurt - Donated Chemical Probes
Scientific Literature
United States Adopted Names (USAN)
WHO Anatomical Therapeutic Chemical (ATC) Classification of Drugs
Withdrawn Drugs
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🔄 Major Data Updates

  • BindingDB Patent Data: tripled assay coverage (4,117 → 13,847 assays).

  • EUbOPEN: new tissue platform data in >20 patient-derived assays.

  • EMA medicines (src_id = 66):

    • First inclusion of biotherapeutics & vaccines from EMA.

    • Pref_name conventions developed for vaccines (e.g. “SARS-COV-2 VIRUS, INACTIVATED”).

  • FDA:

    • Orange Book updated to Nov 2024.

    • New drugs extended to include all new FDA Biological License Applications that were approved in 2023 and 2024

  • Withdrawn drugs: now 327 drug forms, +103 since ChEMBL 35.

  • Black box warnings: NLP pipeline updated (spaCy 3.8.2), applied to 2024–2025 FDA labels.

  • Natural product flag: updated using COCONUT 07/2025.

  • Chemical probe flag: refreshed with chemicalprobes.org + probes-drug.org (July 2025).

  • Protein target names: aligned with UniProt recommended names (~2400 updates).

  • Target types: new 3D CELL CULTURE category for organoids, spheroids, tumoroids.

  • Mechanism vocab: new ACTION_TYPE → GENE EDITING NEGATIVE MODULATOR.

🧬 New Datasets

CHEMBL5604061 ASAP - WNV NS2B-NS3 protease fluorescence dose response
CHEMBL5604062 ASAP - ZIKV NS2B-NS3 protease fluorescence dose response
CHEMBL5604063 ASAP - DENV-2 NS2B-NS3 protease fluorescence dose response
CHEMBL5604064 ASAP - DENV-1 NS2B-NS3 protease fluorescence dose response
CHEMBL5604065 ASAP - DENV-3 NS2B-NS3 protease fluorescence dose response
CHEMBL5604066 ASAP - DENV-4 NS2B-NS3 protease fluorescence dose response
CHEMBL5665443 Enzyme Inhibitor Single Concentration assay results for EUbOPEN Chemogenomics Library
CHEMBL5674860 Optimized Dual-Glo Assay to identify co-culture-induced drug vulnerabilities in 3D CRC models
CHEMBL5598561 ASAP - In vitro binding kinetics
CHEMBL5606458 ASAP - ZIKV NS2B-NS3 protease fluorescence single point
CHEMBL5606459 ASAP - WNV NS2B-NS3 protease fluorescence single point
CHEMBL5606460 ASAP - DENV-2 NS2B-NS3 protease fluorescence single point
CHEMBL5608109 Hepatotoxicity screening of Donated Chemical Probes
CHEMBL5608113 Targeting of CAF-induced therapy resistance in CRC organoid-stroma co-cultures.
CHEMBL5608141 Identification of compartment-specific drug  sensitivities in CRC organoid-stroma co-cultures
CHEMBL5724803 Viability screening in matched tumor and normal assay results for EUbOPEN Chemogenomics Library
CHEMBL5724806 Unraveling interindividual differences and functional consequences of gut microbial metabolism of immunosuppressants
CHEMBL5724914 Linking interpersonal differences in gut microbiota composition and drug biotransformation activity
CHEMBL5724581 Toxicity screen in purified B cell assay results for EUbOPEN Chemogenomics Library
CHEMBL5724696 Autophagy assay results for EUbOPEN Chemogenomics Library
CHEMBL5724558 Image-based profiling of drug vulnerabilities in CRC organoids
CHEMBL5724562 Toxicity screen in isolated B cell assay results for EUbOPEN Chemogenomics Library
CHEMBL5723582 Data for DCP probe T-10430
CHEMBL5723583 Data for DCP probe BAY-9835
CHEMBL5723584 Data for DCP probe C3TD879
CHEMBL5723585 Data for DCP probe JNJ-54082730
CHEMBL5723586 Data for DCP probe BI-1915
CHEMBL5723587 Data for DCP probe BI-113823
CHEMBL5723588 Data for DCP probe JNJ-3738
CHEMBL5724564 Patient-derived NASH model to assess the effects of chemical probes on hepatocyte regenerations

🗄️ Schema Changes

New Tables

  • PESTICIDE_CLASSIFICATION

  • PESTICIDE_CLASS_MAPPING

New Field

  • MOLECULE_DICTIONARY.VETERINARY (flag for veterinary products)

Deprecated (since ChEMBL 35)

  • Tables: FRAC_CLASSIFICATION, HRAC_CLASSIFICATION, IRAC_CLASSIFICATION, MOLECULE_*CLASSIFICATION, RESEARCH_STEM, RESEARCH_COMPANIES

  • Fields: multiple obsolete compound property fields (CX_LOGP, MW_MONOISOTOPIC, Lipinski rule flags, etc.)

 

ChEMBL 36 release notes can be found here.

 

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