chembl-mcp-server

An MCP server that provides tools to search ChEMBL compounds, resolve protein targets, retrieve bioactivity measurements, and access drug pharmacology data including mechanisms of action and clinical indications.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

Community listingLocal stdioSource reviewed; not executedPublished by cyanheads

Vendor documentation

What you can do with it

Search compounds by name, ID, or structure
Retrieve bioactivity measurements for compound-target pairs
Look up drug mechanisms and clinical indications
Resolve protein symbols to ChEMBL target IDs

Source and maintenance

Community listingRegistry 0.5.0

mcp-registry: io.github.cyanheads/chembl-mcp-server@0.5.0 Source repository

Maintenance checked: Oct 31, 2026, 10:59 PM UTC

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

@cyanheads/chembl-mcp-server 0.5.0

npmnpx

@cyanheads/chembl-mcp-server package definition

{
  "version": "0.5.0",
  "transport": "stdio",
  "identifier": "@cyanheads/chembl-mcp-server",
  "runtimeHint": "npx",
  "registryType": "npm",
  "registryBaseUrl": "https://registry.npmjs.org",
  "environmentVariables": [
    {
      "name": "CANVAS_PROVIDER_TYPE",
      "format": "string",
      "default": "duckdb",
      "description": "DataCanvas provider for the bioactivity spill and the chembl_dataframe_* SQL tools; DuckDB is the default. Set to 'none' to disable it: large bioactivity sets then inline a preview but never spill."
    },
    {
      "name": "CHEMBL_API_BASE_URL",
      "format": "string",
      "default": "https://www.ebi.ac.uk/chembl/api/data",
      "description": "Base URL for the ChEMBL REST data API. Override for a private mirror or pinned host."
    },
    {
      "name": "CHEMBL_REQUEST_TIMEOUT_MS",
      "format": "string",
      "default": "30000",
      "description": "Per-attempt timeout in milliseconds for an upstream ChEMBL request, capped by what is left of the call's time budget (45 s for most calls, CHEMBL_SPILL_DEADLINE_MS for a bioactivity spill)."
    },
    {
      "name": "CHEMBL_MAX_PAGE_SIZE",
      "format": "string",
      "default": "1000",
      "description": "Rows per upstream ChEMBL page (max 1000). The bioactivity spill walks pages of this size; an inline bioactivity page requests its limit, capped at this size."
    },
    {
      "name": "CHEMBL_DEFAULT_LIMIT",
      "format": "string",
      "default": "25",
      "description": "Default result limit applied when callers omit it."
    },
    {
      "name": "CHEMBL_MAX_SPILL_ROWS",
      "format": "string",
      "default": "50000",
      "description": "Ceiling on rows chembl_get_bioactivities stages to a DataCanvas table, and so on the upstream page walk behind it. Over the cap the response reports truncated: true and truncated_by: \"row_cap\"."
    },
    {
      "name": "CHEMBL_MAX_CONCURRENT_PAGES",
      "format": "string",
      "default": "4",
      "description": "Most chembl_get_bioactivities spill-page requests in flight at once (1–6), shared by every call on the server."
    },
    {
      "name": "CHEMBL_SPILL_DEADLINE_MS",
      "format": "string",
      "default": "45000",
      "description": "Time budget in milliseconds for one chembl_get_bioactivities spill, its count and page walk (10000–600000). At expiry the rows fetched so far stage with truncated: true and truncated_by: \"time_budget\"."
    },
    {
      "name": "CHEMBL_DATAFRAME_DROP_ENABLED",
      "format": "string",
      "default": "false",
      "description": "Set to 'true' to register the opt-in chembl_dataframe_drop tool (absent from tools/list when off)."
    },
    {
      "name": "MCP_LOG_LEVEL",
      "format": "string",
      "default": "info",
      "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
    }
  ]
}

Tools

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No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

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Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.

Cursor configuration

{
  "mcpServers": {
    "chembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/chembl-mcp-server@0.5.0"
      ],
      "env": {
        "CANVAS_PROVIDER_TYPE": "<YOUR_CANVAS_PROVIDER_TYPE>",
        "CHEMBL_API_BASE_URL": "<YOUR_CHEMBL_API_BASE_URL>",
        "CHEMBL_REQUEST_TIMEOUT_MS": "<YOUR_CHEMBL_REQUEST_TIMEOUT_MS>",
        "CHEMBL_MAX_PAGE_SIZE": "<YOUR_CHEMBL_MAX_PAGE_SIZE>",
        "CHEMBL_DEFAULT_LIMIT": "<YOUR_CHEMBL_DEFAULT_LIMIT>",
        "CHEMBL_MAX_SPILL_ROWS": "<YOUR_CHEMBL_MAX_SPILL_ROWS>",
        "CHEMBL_MAX_CONCURRENT_PAGES": "<YOUR_CHEMBL_MAX_CONCURRENT_PAGES>",
        "CHEMBL_SPILL_DEADLINE_MS": "<YOUR_CHEMBL_SPILL_DEADLINE_MS>",
        "CHEMBL_DATAFRAME_DROP_ENABLED": "<YOUR_CHEMBL_DATAFRAME_DROP_ENABLED>",
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.

Cline configuration

{
  "mcpServers": {
    "chembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/chembl-mcp-server@0.5.0"
      ],
      "env": {
        "CANVAS_PROVIDER_TYPE": "<YOUR_CANVAS_PROVIDER_TYPE>",
        "CHEMBL_API_BASE_URL": "<YOUR_CHEMBL_API_BASE_URL>",
        "CHEMBL_REQUEST_TIMEOUT_MS": "<YOUR_CHEMBL_REQUEST_TIMEOUT_MS>",
        "CHEMBL_MAX_PAGE_SIZE": "<YOUR_CHEMBL_MAX_PAGE_SIZE>",
        "CHEMBL_DEFAULT_LIMIT": "<YOUR_CHEMBL_DEFAULT_LIMIT>",
        "CHEMBL_MAX_SPILL_ROWS": "<YOUR_CHEMBL_MAX_SPILL_ROWS>",
        "CHEMBL_MAX_CONCURRENT_PAGES": "<YOUR_CHEMBL_MAX_CONCURRENT_PAGES>",
        "CHEMBL_SPILL_DEADLINE_MS": "<YOUR_CHEMBL_SPILL_DEADLINE_MS>",
        "CHEMBL_DATAFRAME_DROP_ENABLED": "<YOUR_CHEMBL_DATAFRAME_DROP_ENABLED>",
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.

VS Code configuration

{
  "servers": {
    "chembl-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/chembl-mcp-server@0.5.0"
      ],
      "env": {
        "CANVAS_PROVIDER_TYPE": "<YOUR_CANVAS_PROVIDER_TYPE>",
        "CHEMBL_API_BASE_URL": "<YOUR_CHEMBL_API_BASE_URL>",
        "CHEMBL_REQUEST_TIMEOUT_MS": "<YOUR_CHEMBL_REQUEST_TIMEOUT_MS>",
        "CHEMBL_MAX_PAGE_SIZE": "<YOUR_CHEMBL_MAX_PAGE_SIZE>",
        "CHEMBL_DEFAULT_LIMIT": "<YOUR_CHEMBL_DEFAULT_LIMIT>",
        "CHEMBL_MAX_SPILL_ROWS": "<YOUR_CHEMBL_MAX_SPILL_ROWS>",
        "CHEMBL_MAX_CONCURRENT_PAGES": "<YOUR_CHEMBL_MAX_CONCURRENT_PAGES>",
        "CHEMBL_SPILL_DEADLINE_MS": "<YOUR_CHEMBL_SPILL_DEADLINE_MS>",
        "CHEMBL_DATAFRAME_DROP_ENABLED": "<YOUR_CHEMBL_DATAFRAME_DROP_ENABLED>",
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.

Claude Desktop configuration

{
  "mcpServers": {
    "chembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/chembl-mcp-server@0.5.0"
      ],
      "env": {
        "CANVAS_PROVIDER_TYPE": "<YOUR_CANVAS_PROVIDER_TYPE>",
        "CHEMBL_API_BASE_URL": "<YOUR_CHEMBL_API_BASE_URL>",
        "CHEMBL_REQUEST_TIMEOUT_MS": "<YOUR_CHEMBL_REQUEST_TIMEOUT_MS>",
        "CHEMBL_MAX_PAGE_SIZE": "<YOUR_CHEMBL_MAX_PAGE_SIZE>",
        "CHEMBL_DEFAULT_LIMIT": "<YOUR_CHEMBL_DEFAULT_LIMIT>",
        "CHEMBL_MAX_SPILL_ROWS": "<YOUR_CHEMBL_MAX_SPILL_ROWS>",
        "CHEMBL_MAX_CONCURRENT_PAGES": "<YOUR_CHEMBL_MAX_CONCURRENT_PAGES>",
        "CHEMBL_SPILL_DEADLINE_MS": "<YOUR_CHEMBL_SPILL_DEADLINE_MS>",
        "CHEMBL_DATAFRAME_DROP_ENABLED": "<YOUR_CHEMBL_DATAFRAME_DROP_ENABLED>",
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

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