get_compound_info

Retrieve detailed chemical and biological data for compounds using their ChEMBL ID to support drug discovery and research analysis.

Instructions

Get detailed information for a specific compound by ChEMBL ID

Input Schema

TableJSON Schema

Name	Required	Description	Default
`chembl_id`	Yes	ChEMBL compound ID (e.g., CHEMBL59)

Implementation Reference

src/index.ts:855-876 (handler)

The handler function for the 'get_compound_info' tool. Validates the chembl_id argument and fetches detailed compound information from the ChEMBL API endpoint /molecule/{chembl_id}.json, returning the JSON data as text content.

private async handleGetCompoundInfo(args: any) {
  if (!isValidChemblIdArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid ChEMBL ID arguments');
  }

  try {
    const response = await this.apiClient.get(`/molecule/${args.chembl_id}.json`);
    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(response.data, null, 2),
        },
      ],
    };
  } catch (error) {
    throw new McpError(
      ErrorCode.InternalError,
      `Failed to get compound info: ${error instanceof Error ? error.message : 'Unknown error'}`
    );
  }
}

src/index.ts:410-419 (schema)

The input schema definition for the 'get_compound_info' tool, specifying that it requires a 'chembl_id' string parameter.

  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'],
  },
},

src/index.ts:747-748 (registration)
Registration of the 'get_compound_info' tool handler in the switch statement within the CallToolRequestSchema handler.
```
case 'get_compound_info':
  return await this.handleGetCompoundInfo(args);
```

src/index.ts:90-99 (helper)

Helper validation function used by the get_compound_info handler to validate the input arguments contain a non-empty chembl_id string.

const isValidChemblIdArgs = (
  args: any
): args is { chembl_id: string } => {
  return (
    typeof args === 'object' &&
    args !== null &&
    typeof args.chembl_id === 'string' &&
    args.chembl_id.length > 0
  );
};

src/index.ts:409-736 (registration)

Registration of the 'get_compound_info' tool in the tools array returned by ListToolsRequestSchema handler, including name, description, and input schema.

  {
    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: [],
    },
  },
],

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