Koskamo

PubChem MCP Server

An MCP server that enables agents to search the PubChem chemical database. It supports searching compounds by name, formula, or structure, and fetching detailed physicochemical properties, safety data, bioactivity profiles, drug-food interactions, molecular targets, 3D structures, and external database cross-references.

Package and access

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

PubChem MCP Server logo, by cyanheadsCommunity listingLocal stdioSource reviewed; not executedPublished by cyanheads
Vendor documentation

What you can do with it

  • Search for chemical compounds by name, SMILES, or InChI
  • Retrieve physicochemical properties and safety data for compounds
  • Fetch bioactivity profiles and assay results for specific targets
  • Get 3D structures and 2D diagrams for chemical entities

Source and maintenance

Community listingRegistry 0.8.0
mcp-registry: io.github.cyanheads/pubchem-mcp-server@0.8.0Source repository
Maintenance checked

Packages and installation

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

@cyanheads/pubchem-mcp-server 0.8.0

npmnpx
@cyanheads/pubchem-mcp-server package definition
{
  "version": "0.8.0",
  "transport": "stdio",
  "identifier": "@cyanheads/pubchem-mcp-server",
  "runtimeHint": "npx",
  "registryType": "npm",
  "registryBaseUrl": "https://registry.npmjs.org",
  "environmentVariables": [
    {
      "name": "MCP_LOG_LEVEL",
      "format": "string",
      "default": "info",
      "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

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

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "pubchem-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server@0.8.0"
      ],
      "env": {
        "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": {
    "pubchem-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server@0.8.0"
      ],
      "env": {
        "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": {
    "pubchem-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server@0.8.0"
      ],
      "env": {
        "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": {
    "pubchem-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server@0.8.0"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

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