Koskamo

PubChem MCP

The PubChem MCP server provides access to the NIH PubChem database, offering tools to resolve chemical names to Compound IDs, retrieve standard molecular properties like SMILES and InChI, list synonyms, and fetch pharmacological classifications for over 100 million molecules without requiring authentication.

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Package and access

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

PubChem MCP logo, by PipeworxCommunity listingLocal stdioSource reviewed; not executedPublished by Pipeworx
Vendor documentation

What you can do with it

  • Resolve common chemical or drug names to PubChem CIDs
  • Get standard properties like molecular formula and SMILES for a CID
  • List all synonyms including IUPAC and CAS numbers for a CID
  • Retrieve pharmacological classification trees for drug discovery

Source and maintenance

Community listingRegistry 0.2.0
mcp-registry: io.github.pipeworx-io/pubchem@0.2.0Source repositoryProject website
Maintenance checked

Packages and installation

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

@pipeworx/mcp-pubchem 0.2.0

npm
@pipeworx/mcp-pubchem package definition
{
  "version": "0.2.0",
  "transport": "stdio",
  "identifier": "@pipeworx/mcp-pubchem",
  "registryType": "npm",
  "environmentVariables": [
    {
      "name": "PIPEWORX_API_KEY",
      "description": "Optional Pipeworx API key. Without it calls are anonymous and capped daily; a free key raises the cap."
    }
  ]
}

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": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pubchem@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pubchem@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pubchem@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pubchem@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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