ChEMBL Drug and Compound Lookup

Query the ChEMBL database for drug-like molecules, drug targets, and bioactivity data. ChEMBL is EBI's open database of drug discovery and medicinal chemistry.

IMPORTANT: Query must be a specific drug or compound name

ChEMBL searches by molecule name. Always use a specific drug name or compound identifier (e.g. sotorasib, ibrutinib, CHEMBL1873475). Do NOT pass topic phrases like "kinase inhibitor resistance" — these will return garbage results. If the topic mentions multiple drugs, pick the most specific one.

When NOT to Use This Skill

Do NOT use ChEMBL when the query is any of the following — it will return large biologics, cell therapy entries, or protein records with MW=?, logP=?, phase=-1:

• Biological therapies: cell therapies, stem cells, antibodies, CAR-T, biologics (e.g. "allogeneic mesenchymal stem cells", "anti-PD1 antibody")
• Mechanism or concept phrases: "proximity-induced degradation", "PROTAC linker", "covalent warhead", "undruggable target"
• Disease names without a specific drug: "Alzheimer's disease", "pancreatic cancer", "KRAS oncogenesis"
• Pathway or process terms: "mTOR signaling", "ubiquitin-proteasome pathway", "kinase cascade"

Correct workflow for mechanism-based topics (e.g. PROTAC, degrader, proximity):

1. Search PubMed first with the mechanism query
2. Extract specific small-molecule compound names from the papers (e.g. "ARV-110", "dBET6", "MZ1")
3. Then query ChEMBL with those specific names

Overview

• Search molecules by name or ChEMBL ID
• Retrieve molecular properties, SMILES, drug indications
• Find targets and bioactivity (IC50, Ki, etc.)
• No API key required

Usage

Search by compound or drug name

python3 {baseDir}/scripts/chembl_search.py --query "aspirin"

Get molecule by ChEMBL ID

python3 {baseDir}/scripts/chembl_search.py --chembl-id CHEMBL25

Detailed output

python3 {baseDir}/scripts/chembl_search.py --query "imatinib" --format detailed

Limit search results

python3 {baseDir}/scripts/chembl_search.py --query "kinase inhibitor" --max-results 5

Parameters

Parameter	Description	Default
--query	Compound or drug name or search term	-
--chembl-id	ChEMBL molecule ID (e.g. CHEMBL25)	-
--max-results	Max results for search	10
--format	Output: summary, detailed, json	summary

Output

• Summary: ChEMBL ID, pref_name, molecular formula, MW, SMILES, max_phase
• Detailed: Adds drug type, first approval, indications, targets
• JSON: Full API response

Notes

• ChEMBL IDs look like CHEMBL25, CHEMBL1234567
• Use --query for name or text search
• Use --chembl-id when you know the exact molecule ID