get_target_compounds

Retrieve compounds tested against a specific biological target from ChEMBL database, filtering by activity type and limiting results.

Instructions

Get compounds tested against a specific target

Input Schema

TableJSON Schema

Name	Required	Description
`target_chembl_id`	Yes	ChEMBL target ID
`activity_type`	No	Activity type filter (e.g., IC50, Ki, Kd)
`limit`	No	Number of results to return (1-1000, default: 25)

Implementation Reference

src/index.ts:990-1031 (handler)

Implements the core logic for the 'get_target_compounds' tool. Queries the ChEMBL API /activity endpoint with target_chembl_id filter, processes activities to extract unique molecule_chembl_ids, and returns a summary with compound counts and samples.

private async handleGetTargetCompounds(args: any) {
  if (!args || typeof args.target_chembl_id !== 'string') {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid target compounds arguments');
  }

  try {
    const params: any = {
      target_chembl_id: args.target_chembl_id,
      limit: args.limit || 25,
    };

    if (args.activity_type) {
      params.standard_type = args.activity_type;
    }

    const response = await this.apiClient.get('/activity.json', { params });

    // Extract unique compounds from activities
    const activities = response.data.activities || [];
    const compoundIds = [...new Set(activities.map((a: any) => a.molecule_chembl_id))];

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify({
            target_chembl_id: args.target_chembl_id,
            total_activities: activities.length,
            unique_compounds: compoundIds.length,
            compound_ids: compoundIds.slice(0, 100),
            activities: activities.slice(0, 50),
          }, null, 2),
        },
      ],
    };
  } catch (error) {
    throw new McpError(
      ErrorCode.InternalError,
      `Failed to get target compounds: ${error instanceof Error ? error.message : 'Unknown error'}`
    );
  }
}

src/index.ts:484-495 (registration)

Registers the 'get_target_compounds' tool in the ListToolsRequestSchema response, defining its name, description, and input schema.

  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'],
  },
},

src/index.ts:760-761 (registration)
Dispatches calls to the 'get_target_compounds' tool to its handler function in the CallToolRequestSchema switch statement.
```
case 'get_target_compounds':
  return await this.handleGetTargetCompounds(args);
```

src/index.ts:486-494 (schema)

Defines the input schema (JSON Schema) for validating parameters to the 'get_target_compounds' tool: requires target_chembl_id, optional activity_type and limit.

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'],
},

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