| --- |
| 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](https://www.ebi.ac.uk/chembl/) (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| | `withdrawn_flag` | int64 | Withdrawn from market flag (1/0) | |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 |
|
|
| ```python |
| 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](https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_36/) using [chembl-hf](https://github.com/lukasmki/chembl-hf). |
|
|
| ## License |
|
|
| ChEMBL data is released under [CC BY-SA 4.0](https://creativecommons.org/licenses/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 |
|
|
