| --- |
| pretty_name: 'BindingDB + ChEMBL Binding Affinity Dataset: Ki, Kd, IC50, EC50 Measurements (Normalized)' |
| license: cc-by-sa-3.0 |
| language: |
| - en |
| multilinguality: |
| - monolingual |
| size_categories: |
| - n<1K |
| task_categories: |
| - tabular-regression |
| - tabular-classification |
| annotations_creators: |
| - found |
| language_creators: |
| - found |
| source_datasets: |
| - original |
| tags: |
| - bindingdb |
| - chembl |
| - bioactivity |
| - binding-affinity |
| - drug-discovery |
| - drug-target-interaction |
| - protein-ligand |
| - ki |
| - kd |
| - ic50 |
| - ec50 |
| - cheminformatics |
| - chemistry |
| - biology |
| - medicinal-chemistry |
| - tabular |
| - matrixnorm |
| configs: |
| - config_name: measurements |
| data_files: |
| - split: train |
| path: bindingnorm-bindingdb-202511-chembl_ccbysa/measurements.csv |
| default: true |
| --- |
| |
| # BindingDB + ChEMBL Binding Affinity Dataset: Ki, Kd, IC50, EC50 Measurements (Normalized) |
|
|
| *Release name: BindingDB ChEMBL-Sourced Slice — Normalized Dataset* |
|
|
| Normalized binding-affinity measurements for the **ChEMBL-derived portion of |
| BindingDB** (BindingDB's re-exported ChEMBL records). This repo holds a free toy |
| sample of 1,000 measurements in one CSV file. |
|
|
| ## Free toy sample |
|
|
| This public repo is a deliberately tiny, CSV-only toy sample: 1,000 measurements in one table (no linked tables). It is meant for looking at the schema and running a pipeline once (a toy training run), not for training a real model. The full ChEMBL-sourced slice (1,576,007 measurements) is not in this repo; it is kept in the private repo `williamTLmiller/bindingdb-chembl-binding-affinity-full` (contact energea@energeatech.com). Because it derives from CC BY-SA 3.0 data, any copy of it that is shared stays under CC BY-SA 3.0, the same license as this sample, and the underlying records are also freely available from BindingDB and ChEMBL. |
|
|
| Measurements were picked by a fixed hash of `id`: the first 5 (in hash order) of every endpoint and |
| qualifier combination (so each of the 12 combinations appears), then the rest in hash order. The |
| sample is stable between releases, and its endpoint and qualifier mix differs slightly from the full slice. |
|
|
| ## License and attribution |
|
|
| The underlying measurement data derives from **BindingDB**'s ChEMBL-sourced |
| slice and is redistributed here under **CC BY-SA 3.0**, following BindingDB's |
| license terms for this portion of its data: |
|
|
| - BindingDB: https://www.bindingdb.org — The BindingDB project, University of |
| California, San Diego / Skaggs School of Pharmacy. |
| - ChEMBL: https://www.ebi.ac.uk/chembl/ — EMBL-EBI. The original bioactivity |
| data originate in ChEMBL (itself CC BY-SA 3.0). |
|
|
| If you use this dataset, please cite BindingDB and ChEMBL per their respective |
| citation requirements, and distribute derivatives under CC BY-SA 3.0. The full |
| CC BY-SA 3.0 legal code is in `LICENSE`; `NOTICE` states the credits and what |
| williamTLmiller added. |
|
|
| ## Contents |
|
|
| | file | rows | what it holds | |
| |---|---:|---:| |
| | `bindingnorm-bindingdb-202511-chembl_ccbysa/measurements.csv` | 1,000 | One row per binding measurement: endpoint, value as reported, value in nM and mol/L, the -log10 affinity, qualifier and censoring fields. | |
|
|
| | endpoint | measurements | |
| |---|---:| |
| | `IC50` | 610 | |
| | `Ki` | 246 | |
| | `EC50` | 105 | |
| | `Kd` | 39 | |
|
|
| | relation | censor_kind | measurements | meaning | |
| |---|---:|---:|---:| |
| | `eq` | (empty) | 787 | exact value | |
| | `gt` | `lower_censored` | 183 | reported as `>` a bound: the true value is above `censor_bound` | |
| | `lt` | `upper_censored` | 30 | reported as `<` a bound: the true value is below `censor_bound` | |
| |
| ## Columns |
| |
| - `id`: stable measurement id. |
| - `source_key`: the BindingDB `Reactant_set_id` of the source row; use it to look up the ligand, target, |
| assay and citation in BindingDB (this sample spans 50,001,636 to 51,572,151). |
| - `complex_kind`: `protein_small_molecule` for every row; `evidence_kind`: `experimental` for every row. |
| - `endpoint`: `Ki`, `Kd`, `IC50` or `EC50`. |
| - `raw_value`, `raw_unit`: the value as BindingDB reports it (with any `>` or `<` prefix), in nM. |
| - `relation`: `eq`, `gt` or `lt`, from that prefix. `value`, `unit`: the number in nM. |
| - `molar_value`: the value in mol/L. |
| - `p_value`: the -log10 affinity on the molar scale (pKi, pKd, pIC50 or pEC50), not a statistical p-value; |
| `p_relation` is the qualifier on that scale (it flips, since a larger nM value is a smaller p_value). |
| - `censor_kind`, `censor_bound`, `p_censor_bound`: for qualified values, the kind of bound and the bound |
| in nM and on the p_value scale. |
| - `lower`, `upper`, `p_lower`, `p_upper` (range bounds) and `reported_p_value`, `reported_p_discrepancy` |
| (a source-reported -log10 value and any disagreement with the computed one) are empty in this slice. |
|
|
| In this sample `p_value` runs from −0.33 to 12.00 (median 6.16). One row carries |
| BindingDB's placeholder value 2147483647 nM (`p_value` −0.33); it is kept as |
| reported, so filter it before any modelling. |
|
|
| ## Full slice |
|
|
| The full ChEMBL-sourced slice (BindingDB release 2025-11) has 1,576,007 measurements: IC50 952,432, |
| Ki 400,454, EC50 140,119 and Kd 83,002; 1,310,680 exact, 251,508 `>` and 13,819 `<`. In the full slice |
| 4 rows carry the placeholder value 2147483647 nM, and 141 more carry even larger values (for example |
| 3311311214826 nM and 99999999999999 nM); filter both before modelling. The full slice is not part of |
| this repo and stays under CC BY-SA 3.0 (see above); for access, contact energea@energeatech.com. |
|
|
| ## Scope note |
|
|
| This package is **BindingDB's representation** of ChEMBL-derived measurements — |
| not a native ChEMBL database dump. Assay context is limited to what BindingDB |
| re-exports; richer assay entities live in native ChEMBL releases. |
|
|
| ## Quality checks |
|
|
| Run on the packaged file before upload: unique `id`, `molar_value` equals the nM value times 1e-9, |
| `p_value` equals -log10(`molar_value`), `censor_kind` is set exactly for `>` and `<` values, CSV re-parse. |
|
|
