lukaskim/ChEMBL-36

ChEMBL 36

ChEMBL 36 converted to HuggingFace datasets format. Source data is from the ChEMBL database (EMBL-EBI), a manually curated database of bioactive molecules with drug-like properties.

Dataset configs

molecules (~2.4M rows)

All compounds in ChEMBL with canonical SMILES representations.

Column	Type	Description
chembl_id	string	ChEMBL compound identifier
canonical_smiles	string	Canonical SMILES representation
standard_inchi	string	Standard InChI representation
standard_inchi_key	string	Standard InChI key (27-char hash; use for cross-database deduplication)
molecule_type	string	Compound type (e.g. Small molecule)
max_phase	float64	Highest clinical trial phase reached (0–4; 4 = approved drug; null = not tested)
first_approval	float64	Year of first regulatory approval, if approved
oral	int64	Orally bioavailable flag (1/0)
prodrug	int64	Prodrug flag (1/0)
natural_product	int64	Natural product flag (1/0)
black_box_warning	int64	FDA black-box warning flag (1/0)
withdrawn_flag	int64	Withdrawn from market flag (1/0)
therapeutic_flag	int64	Has a documented therapeutic use (1/0)
mw_freebase	float64	Molecular weight of the free base form
alogp	float64	Calculated lipophilicity (Wildman–Crippen LogP)
hba	float64	Number of hydrogen bond acceptors
hbd	float64	Number of hydrogen bond donors
psa	float64	Polar surface area (Ų)
rtb	float64	Number of rotatable bonds
aromatic_rings	float64	Number of aromatic rings
heavy_atoms	float64	Number of heavy atoms
qed_weighted	float64	Quantitative Estimate of Drug-likeness (0–1)
num_ro5_violations	float64	Number of Lipinski Rule-of-Five violations (0–4)

targets (~15K rows)

Protein targets with amino-acid sequences. Multi-component targets (protein complexes) produce one row per component.

Column	Type	Description
target_chembl_id	string	ChEMBL target identifier
pref_name	string	Preferred target name
target_type	string	Target type (e.g. SINGLE PROTEIN, PROTEIN COMPLEX)
organism	string	Source organism (e.g. Homo sapiens)
tax_id	int64	NCBI taxonomy ID
accession	string	UniProt accession
sequence	string	Amino-acid sequence
gene_names	string	Comma-separated HGNC gene symbol(s) (e.g. EGFR); null for non-gene targets
protein_class_l1	string	Top-level protein family (e.g. Kinase, GPCR); null if unclassified
protein_class_l2	string	Second-level protein family; null if unclassified

molecule_target_pairs (~1–5M rows)

Paired bioactivity records linking compounds to protein targets. Filtered to rows with non-null SMILES, sequence, and pChEMBL value. All included measurements use standard_relation = '=' and standard_units = 'nM'.

Column	Type	Description
chembl_id	string	ChEMBL compound identifier
canonical_smiles	string	Canonical SMILES representation
target_chembl_id	string	ChEMBL target identifier
target_pref_name	string	Preferred target name
organism	string	Target organism
sequence	string	Amino-acid sequence (|-separated for multi-component targets)
standard_type	string	Activity type (e.g. IC50, Ki, Kd)
standard_value	float64	Raw activity value (nM)
pchembl_value	float64	Standardized −log₁₀ activity value
assay_type	string	Assay classification (e.g. B for binding)
confidence_score	int64	Target-assignment confidence 0–9 (9 = direct single-protein assay)

Usage

from datasets import load_dataset

molecules = load_dataset("your-org/chembl-36", "molecules")
targets   = load_dataset("your-org/chembl-36", "targets")
pairs     = load_dataset("your-org/chembl-36", "molecule_target_pairs")

Source

Built from the ChEMBL 36 SQLite release using chembl-hf.

License

ChEMBL data is released under CC BY-SA 4.0. If you use this dataset, please cite the ChEMBL publication:

Zdrazil B, et al. (2024). The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity complementary data resources. Nucleic Acids Research, 52(D1), D1180–D1192. https://doi.org/10.1093/nar/gkad1004