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ChEMBL

Access bioactive molecule data via the ChEMBL API.

Overview

ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It provides:

  • Molecules - Chemical compounds and drugs
  • Targets - Drug targets (proteins, organisms)
  • Activities - Bioassay results
  • Mechanisms - Drug mechanisms of action

Quick Start

from biodbs.fetch import (
    chembl_get_molecule,
    chembl_get_target,
    chembl_search_molecules,
    chembl_get_activities_for_target,
)

# Get molecule
molecule = chembl_get_molecule("CHEMBL25")  # Aspirin

Molecules

Get by ChEMBL ID

from biodbs.fetch import chembl_get_molecule

molecule = chembl_get_molecule("CHEMBL25")

from biodbs.fetch import chembl_search_molecules

results = chembl_search_molecules("aspirin")

Approved Drugs

from biodbs.fetch import chembl_get_approved_drugs

drugs = chembl_get_approved_drugs(max_phase=4)

Targets

Get Target

from biodbs.fetch import chembl_get_target

target = chembl_get_target("CHEMBL1862")  # COX-2

Activities

For Target

from biodbs.fetch import chembl_get_activities_for_target

activities = chembl_get_activities_for_target("CHEMBL1862")

For Molecule

from biodbs.fetch import chembl_get_activities_for_molecule

activities = chembl_get_activities_for_molecule("CHEMBL25")

Drug Information

Indications

from biodbs.fetch import chembl_get_drug_indications

indications = chembl_get_drug_indications("CHEMBL25")

Mechanisms

from biodbs.fetch import chembl_get_mechanisms

mechanisms = chembl_get_mechanisms("CHEMBL25")

Using the Fetcher Class

from biodbs.fetch.ChEMBL import ChEMBL_Fetcher

fetcher = ChEMBL_Fetcher()
molecule = fetcher.get_molecule("CHEMBL25")
  • UniProt - Get detailed protein information for ChEMBL drug targets. Use uniprot_map_ids() to map ChEMBL target IDs to UniProt accessions.
  • PubChem - Look up additional chemical properties (SMILES, InChIKey, safety data) for ChEMBL molecules.
  • ID Translation - Translate between ChEMBL IDs and other chemical identifiers (PubChem CID, InChIKey, SMILES).