alterlab-chembl

ChEMBL Database

Overview

ChEMBL is a manually curated database of bioactive molecules maintained by the European Bioinformatics Institute (EBI), containing over 2 million compounds, 19 million bioactivity measurements, 13,000+ drug targets, and data on approved drugs and clinical candidates. Access and query this data programmatically using the ChEMBL Python client for drug discovery and medicinal chemistry research.

When to Use This Skill

This skill should be used when:

• Compound searches: Finding molecules by name, structure, or properties
• Target information: Retrieving data about proteins, enzymes, or biological targets
• Bioactivity data: Querying IC50, Ki, EC50, or other activity measurements
• Drug information: Looking up approved drugs, mechanisms, or indications
• Structure searches: Performing similarity or substructure searches
• Cheminformatics: Analyzing molecular properties and drug-likeness
• Target-ligand relationships: Exploring compound-target interactions
• Drug discovery: Identifying inhibitors, agonists, or bioactive molecules

Installation and Setup

Python Client

The ChEMBL Python client is required for programmatic access:

uv pip install chembl_webresource_client

Basic Usage Pattern

from chembl_webresource_client.new_client import new_client

# Access different endpoints
molecule = new_client.molecule
target = new_client.target
activity = new_client.activity
drug = new_client.drug

Core Capabilities

1. Molecule Queries

Retrieve by ChEMBL ID:

molecule = new_client.molecule
aspirin = molecule.get('CHEMBL25')

Search by name:

results = molecule.filter(pref_name__icontains='aspirin')

Filter by properties:

# Find small molecules (MW <= 500) with favorable LogP
results = molecule.filter(
    molecule_properties__mw_freebase__lte=500,
    molecule_properties__alogp__lte=5
)

2. Target Queries

Retrieve target information:

target = new_client.target
egfr = target.get('CHEMBL203')