ChEMBL MCP Server

Instructions

Implementation Reference

• src/index.ts:909-933 (handler)

  The handler function for the 'get_compound_structure' tool. Validates input, fetches compound data from ChEMBL API, extracts and returns structure information (SMILES, InChI, etc.) in the requested format.
  private async handleGetCompoundStructure(args: any) { if (!args || typeof args.chembl_id !== 'string') { throw new McpError(ErrorCode.InvalidParams, 'Invalid arguments'); } try { const response = await this.apiClient.get(`/molecule/${args.chembl_id}.json`); const compound = response.data; return { content: [ { type: 'text', text: JSON.stringify({ chembl_id: compound.molecule_chembl_id, structures: compound.molecule_structures || {}, requested_format: args.format || 'smiles' }, null, 2), }, ], }; } catch (error) { throw new McpError(ErrorCode.InternalError, `Failed to get structure: ${error instanceof Error ? error.message : 'Unknown error'}`); } }
• src/index.ts:433-443 (schema)

  The input schema definition for the 'get_compound_structure' tool, specifying parameters chembl_id (required) and optional format.
  name: 'get_compound_structure', description: 'Retrieve chemical structure information in various formats', inputSchema: { type: 'object', properties: { chembl_id: { type: 'string', description: 'ChEMBL compound ID' }, format: { type: 'string', enum: ['smiles', 'inchi', 'molfile', 'sdf'], description: 'Structure format (default: smiles)' }, }, required: ['chembl_id'], }, },
• src/index.ts:751-752 (registration)

  The dispatch/registration in the CallToolRequestSchema switch statement that routes calls to the handleGetCompoundStructure handler.
  case 'get_compound_structure': return await this.handleGetCompoundStructure(args);
• src/index.ts:393-737 (registration)

  The tool is registered/listed in the ListToolsRequestSchema handler, including its name, description, and schema.
  this.server.setRequestHandler(ListToolsRequestSchema, async () => ({ tools: [ // Core Chemical Search & Retrieval (5 tools) { name: 'search_compounds', description: 'Search ChEMBL database for compounds by name, synonym, or identifier', inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'Search query (compound name, synonym, or identifier)' }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, offset: { type: 'number', description: 'Number of results to skip (default: 0)', minimum: 0 }, }, required: ['query'], }, }, { name: 'get_compound_info', description: 'Get detailed information for a specific compound by ChEMBL ID', inputSchema: { type: 'object', properties: { chembl_id: { type: 'string', description: 'ChEMBL compound ID (e.g., CHEMBL59)' }, }, required: ['chembl_id'], }, }, { name: 'search_by_inchi', description: 'Search for compounds by InChI key or InChI string', inputSchema: { type: 'object', properties: { inchi: { type: 'string', description: 'InChI key or InChI string' }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: ['inchi'], }, }, { name: 'get_compound_structure', description: 'Retrieve chemical structure information in various formats', inputSchema: { type: 'object', properties: { chembl_id: { type: 'string', description: 'ChEMBL compound ID' }, format: { type: 'string', enum: ['smiles', 'inchi', 'molfile', 'sdf'], description: 'Structure format (default: smiles)' }, }, required: ['chembl_id'], }, }, { name: 'search_similar_compounds', description: 'Find chemically similar compounds using Tanimoto similarity', inputSchema: { type: 'object', properties: { smiles: { type: 'string', description: 'SMILES string of the query molecule' }, similarity: { type: 'number', description: 'Similarity threshold (0-1, default: 0.7)', minimum: 0, maximum: 1 }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: ['smiles'], }, }, // Target Analysis & Drug Discovery (5 tools) { name: 'search_targets', description: 'Search for biological targets by name or type', inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'Target name or search query' }, target_type: { type: 'string', description: 'Target type filter (e.g., SINGLE PROTEIN, PROTEIN COMPLEX)' }, organism: { type: 'string', description: 'Organism filter' }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: ['query'], }, }, { name: 'get_target_info', description: 'Get detailed information for a specific target by ChEMBL target ID', inputSchema: { type: 'object', properties: { chembl_id: { type: 'string', description: 'ChEMBL target ID (e.g., CHEMBL2095173)' }, }, required: ['chembl_id'], }, }, { name: 'get_target_compounds', description: 'Get compounds tested against a specific target', inputSchema: { type: 'object', properties: { target_chembl_id: { type: 'string', description: 'ChEMBL target ID' }, activity_type: { type: 'string', description: 'Activity type filter (e.g., IC50, Ki, Kd)' }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: ['target_chembl_id'], }, }, { name: 'search_by_uniprot', description: 'Find ChEMBL targets by UniProt accession', inputSchema: { type: 'object', properties: { uniprot_id: { type: 'string', description: 'UniProt accession number' }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: ['uniprot_id'], }, }, { name: 'get_target_pathways', description: 'Get biological pathways associated with a target', inputSchema: { type: 'object', properties: { target_chembl_id: { type: 'string', description: 'ChEMBL target ID' }, }, required: ['target_chembl_id'], }, }, // Bioactivity & Assay Data (5 tools) { name: 'search_activities', description: 'Search bioactivity measurements and assay results', inputSchema: { type: 'object', properties: { target_chembl_id: { type: 'string', description: 'ChEMBL target ID filter' }, assay_chembl_id: { type: 'string', description: 'ChEMBL assay ID filter' }, molecule_chembl_id: { type: 'string', description: 'ChEMBL compound ID filter' }, activity_type: { type: 'string', description: 'Activity type (e.g., IC50, Ki, EC50)' }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: [], }, }, { name: 'get_assay_info', description: 'Get detailed information for a specific assay by ChEMBL assay ID', inputSchema: { type: 'object', properties: { chembl_id: { type: 'string', description: 'ChEMBL assay ID (e.g., CHEMBL1217643)' }, }, required: ['chembl_id'], }, }, { name: 'search_by_activity_type', description: 'Find bioactivity data by specific activity type and value range', inputSchema: { type: 'object', properties: { activity_type: { type: 'string', description: 'Activity type (e.g., IC50, Ki, EC50, Kd)' }, min_value: { type: 'number', description: 'Minimum activity value' }, max_value: { type: 'number', description: 'Maximum activity value' }, units: { type: 'string', description: 'Units filter (e.g., nM, uM)' }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: ['activity_type'], }, }, { name: 'get_dose_response', description: 'Get dose-response data and activity profiles for compounds', inputSchema: { type: 'object', properties: { molecule_chembl_id: { type: 'string', description: 'ChEMBL compound ID' }, target_chembl_id: { type: 'string', description: 'ChEMBL target ID (optional filter)' }, }, required: ['molecule_chembl_id'], }, }, { name: 'compare_activities', description: 'Compare bioactivity data across multiple compounds or targets', inputSchema: { type: 'object', properties: { molecule_chembl_ids: { type: 'array', items: { type: 'string' }, description: 'Array of ChEMBL compound IDs (2-10)', minItems: 2, maxItems: 10 }, target_chembl_id: { type: 'string', description: 'ChEMBL target ID for comparison' }, activity_type: { type: 'string', description: 'Activity type for comparison' }, }, required: ['molecule_chembl_ids'], }, }, // Drug Development & Clinical Data (4 tools) { name: 'search_drugs', description: 'Search for approved drugs and clinical candidates', inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'Drug name or search query' }, development_phase: { type: 'string', description: 'Development phase filter (e.g., Approved, Phase III)' }, therapeutic_area: { type: 'string', description: 'Therapeutic area filter' }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: ['query'], }, }, { name: 'get_drug_info', description: 'Get drug development status and clinical trial information', inputSchema: { type: 'object', properties: { chembl_id: { type: 'string', description: 'ChEMBL compound ID' }, }, required: ['chembl_id'], }, }, { name: 'search_drug_indications', description: 'Search for therapeutic indications and disease areas', inputSchema: { type: 'object', properties: { indication: { type: 'string', description: 'Disease or indication search term' }, drug_type: { type: 'string', description: 'Drug type filter (e.g., Small molecule, Antibody)' }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: ['indication'], }, }, { name: 'get_mechanism_of_action', description: 'Get mechanism of action and target interaction data', inputSchema: { type: 'object', properties: { chembl_id: { type: 'string', description: 'ChEMBL compound ID' }, }, required: ['chembl_id'], }, }, // Chemical Property Analysis (4 tools) { name: 'analyze_admet_properties', description: 'Analyze ADMET properties (Absorption, Distribution, Metabolism, Excretion, Toxicity)', inputSchema: { type: 'object', properties: { chembl_id: { type: 'string', description: 'ChEMBL compound ID' }, }, required: ['chembl_id'], }, }, { name: 'calculate_descriptors', description: 'Calculate molecular descriptors and physicochemical properties', inputSchema: { type: 'object', properties: { chembl_id: { type: 'string', description: 'ChEMBL compound ID' }, smiles: { type: 'string', description: 'SMILES string (alternative to ChEMBL ID)' }, }, required: [], }, }, { name: 'predict_solubility', description: 'Predict aqueous solubility and permeability properties', inputSchema: { type: 'object', properties: { chembl_id: { type: 'string', description: 'ChEMBL compound ID' }, smiles: { type: 'string', description: 'SMILES string (alternative to ChEMBL ID)' }, }, required: [], }, }, { name: 'assess_drug_likeness', description: 'Assess drug-likeness using Lipinski Rule of Five and other metrics', inputSchema: { type: 'object', properties: { chembl_id: { type: 'string', description: 'ChEMBL compound ID' }, smiles: { type: 'string', description: 'SMILES string (alternative to ChEMBL ID)' }, }, required: [], }, }, // Advanced Search & Cross-References (4 tools) { name: 'substructure_search', description: 'Find compounds containing specific substructures', inputSchema: { type: 'object', properties: { smiles: { type: 'string', description: 'SMILES string of the substructure query' }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: ['smiles'], }, }, { name: 'batch_compound_lookup', description: 'Process multiple ChEMBL IDs efficiently', inputSchema: { type: 'object', properties: { chembl_ids: { type: 'array', items: { type: 'string' }, description: 'Array of ChEMBL compound IDs (1-50)', minItems: 1, maxItems: 50 }, }, required: ['chembl_ids'], }, }, { name: 'get_external_references', description: 'Get links to external databases (PubChem, DrugBank, PDB, etc.)', inputSchema: { type: 'object', properties: { chembl_id: { type: 'string', description: 'ChEMBL compound or target ID' }, }, required: ['chembl_id'], }, }, { name: 'advanced_search', description: 'Complex queries with multiple chemical and biological filters', inputSchema: { type: 'object', properties: { min_mw: { type: 'number', description: 'Minimum molecular weight (Da)', minimum: 0 }, max_mw: { type: 'number', description: 'Maximum molecular weight (Da)', minimum: 0 }, min_logp: { type: 'number', description: 'Minimum LogP value' }, max_logp: { type: 'number', description: 'Maximum LogP value' }, max_hbd: { type: 'number', description: 'Maximum hydrogen bond donors', minimum: 0 }, max_hba: { type: 'number', description: 'Maximum hydrogen bond acceptors', minimum: 0 }, limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 }, }, required: [], }, }, ], }));