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ChEMBL

Explore 2M+ drugs and compounds. Find approved drugs, bioactivity data, mechanisms of action, and drug-target interactions.

Key Tools

chembl_search_molecules — Find drugs by name

{
  "name": "chembl_search_molecules",
  "arguments": {
    "query": "eculizumab",
    "max_results": 10
  }
}

Arguments:

  • query (str): Drug name or synonym
  • max_results (int, optional): Results to return

Returns: Molecules with ChEMBL ID, IUPAC name, synonyms, drug indication

chembl_get_molecule — Get molecule details

{
  "name": "chembl_get_molecule",
  "arguments": {
    "molecule_id": "CHEMBL2397693"
  }
}

Arguments:

  • molecule_id (str): ChEMBL molecule ID

Returns: Full molecule data: structure, molecular weight, LogP, MeSH terms, indications, ATC codes, max phase reached

chembl_search_targets — Find proteins by name

{
  "name": "chembl_search_targets",
  "arguments": {
    "query": "acetylcholine receptor",
    "max_results": 10
  }
}

Arguments:

  • query (str): Protein/gene name
  • max_results (int, optional): Results to return

Returns: Target proteins with ChEMBL ID, target type, organism

chembl_get_target — Get protein details

{
  "name": "chembl_get_target",
  "arguments": {
    "target_id": "CHEMBL612"
  }
}

Returns: Target metadata: synonyms, organism, UniProt ID, cross-references

chembl_find_drugs_by_target — Get all drugs targeting a protein

{
  "name": "chembl_find_drugs_by_target",
  "arguments": {
    "target_name": "CHRNE",
    "include_all_mechanisms": true,
    "max_results": 20
  }
}

Arguments:

  • target_name (str): Gene symbol or protein name
  • include_all_mechanisms (bool, optional): Include all known mechanisms (not just primary)
  • max_results (int, optional): Drugs to return

Returns: Drugs targeting the gene with mechanism, max phase, clinical status

chembl_find_drugs_by_indication — Get drugs for a disease

{
  "name": "chembl_find_drugs_by_indication",
  "arguments": {
    "indication": "myasthenia gravis",
    "max_results": 20
  }
}

Arguments:

  • indication (str): Disease/indication name
  • max_results (int, optional): Results to return

Returns: Approved and investigational drugs with indication

chembl_get_activities — Get bioactivity data

{
  "name": "chembl_get_activities",
  "arguments": {
    "molecule_id": "CHEMBL25",
    "target_id": "CHEMBL612",
    "max_results": 50
  }
}

Arguments:

  • molecule_id (str, optional): Drug identifier
  • target_id (str, optional): Protein identifier
  • max_results (int, optional): Activities to return

Returns: Bioactivity data: assay type, measurement, units, value, confidence

chembl_get_mechanism — Get drug mechanism of action

{
  "name": "chembl_get_mechanism",
  "arguments": {
    "molecule_id": "CHEMBL2397693"
  }
}

Returns: Mechanism(s) of action with target, organism, primary/secondary status

chembl_get_drug_indications — Get all indications for drug

{
  "name": "chembl_get_drug_indications",
  "arguments": {
    "molecule_id": "CHEMBL2397693"
  }
}

Returns: FDA-approved and investigational indications

Use Cases

Find Approved Drugs for Disease

{
  "name": "chembl_find_drugs_by_indication",
  "arguments": {
    "indication": "myasthenia gravis",
    "max_results": 20
  }
}

Find Unapproved Drugs Targeting Gene

{
  "name": "chembl_find_drugs_by_target",
  "arguments": {
    "target_name": "CHRNE",
    "include_all_mechanisms": true,
    "max_results": 30
  }
}

Get Bioactivity Data for Target

{
  "name": "chembl_get_activities",
  "arguments": {
    "target_id": "CHEMBL612",
    "max_results": 100
  }
}

Returns all compounds tested against this target with potency (IC50, Kd, etc.)

Find Drug Mechanism of Action

{
  "name": "chembl_get_mechanism",
  "arguments": {
    "molecule_id": "CHEMBL2397693"
  }
}

Repurposing Screening

For a list of genes:

  1. Search each gene in ChEMBL (find_drugs_by_target)
  2. Find all compounds tested against target (get_activities)
  3. Cross-reference with clinical trials (ctg_search_by_intervention)
  4. Check safety profile (openfda_search_adverse_events)

Data Fields

Molecule data includes:

  • SMILES string (chemical structure)
  • Molecular weight, LogP (lipophilicity), HBA/HBD (ADME properties)
  • Max phase reached (approved vs investigational)
  • ATC codes (drug classification)
  • Indications (FDA-approved uses)
  • Black box warnings
  • Synonyms and trade names

Target data includes:

  • Protein type (enzyme, kinase, GPCR, antibody, etc.)
  • Organism (human, mouse, rat, etc.)
  • Uniprot ID (link to full protein info)
  • Bioassay count (how much data?)

Bioactivity data includes:

  • Assay type (binding, functional, etc.)
  • Measurement type (IC50, Kd, EC50, etc.)
  • Value and units
  • Confidence score

Workflow: Drug Repurposing Screen

  1. Pick target gene (from OpenTargets or UniProt)
  2. Find all drugs targeting it (find_drugs_by_target)
  3. Get bioactivity data (get_activities) — which are most potent?
  4. Check indications (get_drug_indications) — what's it approved for?
  5. Check mechanism (get_mechanism) — how does it work?
  6. Check safety (openfda_search_adverse_events) — any red flags?
  7. Search trials (ctg_search_by_intervention) — any ongoing trials?
  8. Search literature (pubmed_search_articles) — any recent data?

Notes

  • Coverage: Approved drugs, clinical candidates, research compounds
  • Bioactivity: 15M+ activity records across 10K+ assays
  • Max phase: Highest development stage reached (approved vs Phase 1/2/3)
  • Mechanism annotation: Human-curated (high quality)
  • Structure: Chemical structures in SMILES format (machine-readable)

Rate Limits

  • No API key required
  • Public endpoint
  • Results cached (30-day TTL)

Examples

Example 1: Find all drugs approved for Myasthenia Gravis

{
  "method": "tools/call",
  "params": {
    "name": "chembl_find_drugs_by_indication",
    "arguments": {
      "indication": "myasthenia gravis",
      "max_results": 20
    }
  }
}

Example 2: Get mechanism of action for eculizumab (Soliris)

{
  "method": "tools/call",
  "params": {
    "name": "chembl_search_molecules",
    "arguments": {
      "query": "eculizumab",
      "max_results": 1
    }
  }
}

Then use molecule_id from result:

{
  "method": "tools/call",
  "params": {
    "name": "chembl_get_mechanism",
    "arguments": {
      "molecule_id": "CHEMBL2397693"
    }
  }
}

Example 3: Find all compounds tested against acetylcholine receptor

{
  "method": "tools/call",
  "params": {
    "name": "chembl_search_targets",
    "arguments": {
      "query": "acetylcholine receptor",
      "max_results": 5
    }
  }
}

Then get activities:

{
  "method": "tools/call",
  "params": {
    "name": "chembl_get_activities",
    "arguments": {
      "target_id": "CHEMBL612",
      "max_results": 100
    }
  }
}

Example 4: Repurposing check for CHRNE gene

{
  "method": "tools/call",
  "params": {
    "name": "chembl_find_drugs_by_target",
    "arguments": {
      "target_name": "CHRNE",
      "include_all_mechanisms": true,
      "max_results": 30
    }
  }
}