license: cc-by-sa-4.0
pretty_name: ChEMBL 36
tags:
- chemistry
- drug-discovery
- biology
- smiles
- proteins
- bioactivity
size_categories:
- 1M<n<10M
configs:
- config_name: molecules
data_files: molecules/train-*.parquet
- config_name: targets
data_files: targets/train-*.parquet
- config_name: molecule_target_pairs
data_files: molecule_target_pairs/train-*.parquet
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int64 | Withdrawn from market flag (1/0) |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