ChEMBL Connector#
The ChEMBL Connector gives Claude access to the ChEMBL Database, a manually curated resource of bioactive drug-like compounds with quantitative binding and functional data against biological targets.
What You Can Do#
With this connector, Claude can help you:
Search for compounds by name or chemical structure
Retrieve bioactivity data (IC50, EC50, Ki values)
Find drug targets and mechanisms of action
Access ADMET properties for drug candidates
Discover approved drugs by indication
Research structure-activity relationships
Data Source: ChEMBL Database v34 (EMBL-EBI)
MCP Endpoint: https://mcp.deepsense.ai/chembl/mcp Coverage: 2.4+ million compounds, 1.5+ million assays, 16+ million activities
Getting Started#
Adding the Connector to Claude#
Open Claude’s Connector Settings
In Claude Desktop, select your profile icon in the bottom left
Navigate to Settings → Connectors
Find the ChEMBL Connector
Browse the available connectors catalogue
Search for “ChEMBL” or find it under Life Sciences connectors
Enable the Connector
Click on the ChEMBL Connector
Click “Enable” or “Add Connector”
The connector will be activated immediately
No authentication required - the connector works immediately after enabling
Verify the Connection
Ask Claude: “What is the IC50 of imatinib against BCR-ABL?”
Claude should use the ChEMBL connector to find bioactivity data
Available Tools#
1. Compound Search#
What it does: Searches for chemical compounds by name, SMILES structure, or ChEMBL ID.
Use it for:
Finding compounds by drug name
Looking up compounds by chemical structure
Getting molecular properties
Checking clinical development status
Finding chemical identifiers
Example queries:
“Find information about aspirin”
“Search for imatinib in ChEMBL”
“What is the molecular weight of pembrolizumab?”
“Look up compound CHEMBL25”
“Find compounds similar to gefitinib”
What Claude will do:
Search the ChEMBL database
Return compound ChEMBL IDs
Provide molecular properties:
Molecular weight
LogP (lipophilicity)
Number of hydrogen bond donors/acceptors
Rotatable bonds
Rule of Five violations
Show clinical development phase (preclinical through approved)
Include chemical structure information (SMILES, InChI)
2. Target Search#
What it does: Searches for biological targets (proteins, genes, receptors).
Use it for:
Finding drug targets
Looking up proteins by gene symbol
Understanding target classification
Finding related targets in a family
Example queries:
“Find the EGFR target in ChEMBL”
“Search for BCR-ABL protein”
“What targets are in the kinase family?”
“Look up target CHEMBL203”
What Claude will do:
Search for matching targets
Return target ChEMBL IDs
Provide target information:
Target type (single protein, protein complex, family)
Organism (species)
Gene symbols
UniProt and Ensembl IDs
Show protein family classification
3. Get Bioactivity#
What it does: Retrieves bioactivity data for compound-target interactions.
Use it for:
Finding IC50, EC50, or Ki values
Comparing compound potencies
Assessing selectivity profiles
Identifying off-target activities
Example queries:
“What is the IC50 of imatinib against BCR-ABL?”
“Show me bioactivity data for aspirin”
“Find Ki values for gefitinib”
“What targets does pembrolizumab bind to?”
“Compare IC50 values of erlotinib and gefitinib”
What Claude will do:
Retrieve activity data for the compound
Show quantitative measurements:
IC50 (half maximal inhibitory concentration)
EC50 (half maximal effective concentration)
Ki (inhibition constant)
Kd (dissociation constant)
Values in nM (nanomolar) or μM (micromolar)
Indicate target names and organisms
Provide assay information and confidence scores
Include data quality indicators
4. Get Mechanism#
What it does: Retrieves mechanism of action and target binding information.
Use it for:
Understanding how drugs work
Identifying primary and secondary targets
Finding action types (inhibitor, agonist, antagonist)
Researching polypharmacology
Example queries:
“How does imatinib work?”
“What is the mechanism of action of aspirin?”
“What targets does gefitinib inhibit?”
“Show me the mechanism for pembrolizumab”
What Claude will do:
Retrieve mechanism of action descriptions
Identify primary target(s)
Show action type:
Inhibitor (decreases activity)
Agonist (activates target)
Antagonist (blocks activation)
Blocker, Modulator, Activator, etc.
Indicate clinical development phase
Provide references to publications
5. Drug Search#
What it does: Searches for approved drugs by indication or name.
Use it for:
Finding approved drugs for diseases
Researching therapeutic indications
Drug repurposing research
Market analysis
Competitive intelligence
Example queries:
“Find approved drugs for breast cancer”
“What drugs treat hypertension?”
“Search for diabetes medications”
“Show me approved kinase inhibitors”
What Claude will do:
Search approved drugs (max_phase=4)
Return drug information:
Drug names and synonyms
ChEMBL IDs
Therapeutic indications
Approval years
Primary targets
Mechanisms of action
Filter by development phase
Group by indication
6. Get ADMET#
What it does: Retrieves ADMET properties (Absorption, Distribution, Metabolism, Excretion, Toxicity).
Use it for:
Predicting drug-likeness
Assessing safety liabilities
Comparing pharmacokinetic profiles
Lead optimization
Understanding metabolic stability
Example queries:
“What are the ADMET properties of imatinib?”
“Show me pharmacokinetic data for aspirin”
“Is gefitinib orally bioavailable?”
“What is the LogP of pembrolizumab?”
What Claude will do:
Retrieve calculated molecular properties:
ALogP: Lipophilicity (optimal: 1-3 for oral drugs)
Molecular Weight: Full molecular weight in Da
PSA: Polar surface area (<140 for oral, <90 for CNS)
HBA/HBD: H-bond acceptors/donors (Rule of 5: ≤10/≤5)
Rotatable Bonds: <10 for good oral bioavailability
Aromatic Rings: <4 recommended
Rule of 5 Violations: 0-1 preferred for oral drugs
QED: Drug-likeness score (0-1, higher is better)
Explain property implications for drug development
Usage Examples#
Example 1: Researching a Drug Target#
You: “I’m interested in EGFR inhibitors. What are the IC50 values of gefitinib and erlotinib against EGFR?”
Claude will:
Use Target Search to find EGFR target ID
Use Compound Search to find gefitinib and erlotinib
Use Get Bioactivity for each compound against EGFR
Compare IC50 values
Explain relative potencies
Example 2: Drug Repurposing#
You: “Find approved drugs that target BCR-ABL. I want to explore repurposing opportunities.”
Claude will:
Use Target Search to find BCR-ABL
Use Drug Search filtered by approved status
Use Get Bioactivity to show potencies
Use Get Mechanism to understand action types
List current indications for each drug
Example 3: Lead Optimization#
You: “I have a compound with ChEMBL ID CHEMBL123456. What are its drug-like properties and how potent is it?”
Claude will:
Use Compound Search to get compound details
Use Get ADMET to show molecular properties
Use Get Bioactivity to find target activities
Assess Rule of 5 violations
Suggest property improvements if needed
Need Help?#
For issues or questions about the ChEMBL Connector, see our Troubleshooting Guide.