chembl_bioactivity — ChEMBL compound-target bioactivities (2026)

Description

A bipartite network of the compounds and the biological targets of ChEMBL, the manually curated database of bioactive molecules with drug-like properties of the European Bioinformatics Institute (EMBL-EBI), release 37 (May 2026). An edge is a bioactivity measurement of a compound in an assay on a target, e.g. an inhibition constant ($K_i$) or a half-maximal inhibitory concentration (IC50), so that a compound and a target are connected by as many edges as there are measurements. The measurements are mostly extracted from the scientific literature (medicinal chemistry journals), and also come from deposited datasets (e.g. PubChem BioAssays, patents via BindingDB and SureChEMBL, screening campaigns against malaria and other neglected diseases).

The targets are mostly single proteins, but also protein complexes and families, nucleic acids, cell lines, tissues and whole organisms, as given by the node property target_type; the compounds are mostly small molecules, but also e.g. antibodies and other proteins. All the 24.5 million activities of the release are included, also those with a comment about their validity (e.g. a possible transcription error, or units that are outside the typical range for that activity type) and those flagged as possible duplicates, as well as activities without a numerical value (e.g. those only reported as active or inactive). The assays and documents of the activities (other than the year of publication), their original (unstandardized) values, and the structures of the compounds are not included.

The network has the following properties:

(Node) is_compound: whether the node is a compound (otherwise it is a target).
(Node) chembl_id: the ChEMBL identifier of the compound or target (e.g. CHEMBL25, aspirin; CHEMBL203, the epidermal growth factor receptor), whose page is https://www.ebi.ac.uk/chembl/explore/compound/<chembl_id> or https://www.ebi.ac.uk/chembl/explore/target/<chembl_id>.
(Node) name: the preferred name of the compound or target (empty for most compounds, which have no name).
(Node) molecule_type (compounds): the type of the compound, e.g. Small molecule, Protein, Antibody (empty for targets).
(Node) max_phase (compounds): the maximum clinical phase reached by the compound: 4 (approved drug), 3, 2, 1, 0.5 (early phase 1), or -1 (preclinical or unknown, also for targets).
(Node) target_type (targets): the type of the target, e.g. SINGLE PROTEIN, PROTEIN COMPLEX, CELL-LINE, ORGANISM (empty for compounds).
(Node) organism (targets): the organism of the target (empty if none, and for compounds).
(Node) tax_id (targets): the NCBI taxonomy identifier of the organism (-1 if none, and for compounds).
(Edge) standard_type: the type of the measurement, standardized, e.g. IC50, Ki, Potency, Inhibition.
(Edge) standard_relation: the relation of the measured value: =, <, >, <=, >=, ~ (empty if there is no value).
(Edge) standard_value: the measured value, standardized (NaN if there is none).
(Edge) standard_units: the units of the value, e.g. nM, % (empty if none).
(Edge) pchembl_value: the negative logarithm (base 10) of the molar concentration (e.g. IC50, Ki, EC50), for comparable measures of potency (NaN if not applicable).
(Edge) assay_type: the type of the assay: B (binding), F (functional), A (absorption, distribution, metabolism and excretion), T (toxicity), P (physicochemical) or U (unclassified).
(Edge) year: the year of publication of the document the measurement comes from (-1 if not known, e.g. for deposited datasets).
(Edge) data_validity_comment: a comment on the validity of the measurement, e.g. Outside typical range, Potential transcription error (empty if none).
(Edge) potential_duplicate: whether the measurement is a possible duplicate of one reported in another document.

Tags

Biological Chemical Drug interactions Weighted Multigraph Metadata

Added

2026-10-28

Citation

B. Zdrazil et al., "The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods." Nucleic Acids Research 52, D1180-D1192 (2024) 10.1093/nar/gkad1004 Sci-Hub
D. Mendez et al., "ChEMBL: towards direct deposition of bioassay data." Nucleic Acids Research 47, D930-D940 (2019) 10.1093/nar/gky1075 Sci-Hub

Upstream URL OK

https://www.ebi.ac.uk/chembl/
https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_37/

Upstream license

CC BY-SA 3.0 (ChEMBL data is from http://www.ebi.ac.uk/chembl; the version of ChEMBL is chembl_37), https://creativecommons.org/licenses/by-sa/3.0/

Networks

Tip: hover over a column header for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
chembl_bioactivity	2,939,700	24,527,044	16.69	1704.28	1482.97	551.02	-0.12	0.00	12	0.96	Undirected	Bipartite	is_compound chembl_id name molecule_type max_phase target_type organism tax_id	standard_type standard_relation standard_value standard_units pchembl_value assay_type year data_validity_comment potential_duplicate	75.1 MiB	195.4 MiB	189.9 MiB	158.1 MiB