Pubchem MCP Server

🚀 PubChem MCP Server

A Model Context Protocol (MCP) server for retrieving chemical compound data from the PubChem database.

🚀 Quick Start

The PubChem MCP Server is an MCP server implemented in Python, allowing AI models to query compound information in the PubChem database. It provides convenient access to compound properties, 2D structures, and 3D molecular coordinates through a standard MCP interface.

✨ Features

• Query compounds by name or PubChem CID.
• Retrieve comprehensive compound data, including:
  • IUPAC name
  • Molecular formula
  • Molecular weight
  • SMILES notation
  • InChI and InChIKey
• Support multiple output formats:
  • JSON (default)
  • CSV
  • XYZ (3D structure)
• Built - in caching system to improve performance.
• Automatic retry mechanism to ensure API reliability.
• Backup 3D structure generation when PubChem 3D is unavailable.

📦 Installation

Install from Source Code

# Clone the repository
git clone https://github.com/yourusername/pubchem-mcp-server.git
cd pubchem-mcp-server/python_version

# Install the package
pip install -e .

# For enhanced 3D structure handling, install with RDKit
pip install -e ".[rdkit]"

📚 Documentation

MCP Configuration

To use the server with Claude or other MCP - supported AI models, add the following content to your MCP configuration file:

{
  "mcpServers": {
    "pubchem": {
      "command": "python3",
      "args": ["/path/to/pubchem-mcp-server/python_version/mcp_server.py"],
      "env": {
        "PYTHONUNBUFFERED": "1"
      },
      "disabled": false,
      "autoApprove": [
        "get_pubchem_data",
        "download_structure"
      ]
    }
  }
}

Available Tools

get_pubchem_data

Retrieve chemical compound structure and property data.

Parameters:

• query (required): Compound name or PubChem CID.
• format (optional): Output format - "JSON" (default), "CSV", or "XYZ".
• include_3d (optional): Whether to include the 3D structure (only valid when the format is "XYZ").

Example Usage:

<use_mcp_tool>
<server_name>pubchem</server_name>
<tool_name>get_pubchem_data</tool_name>
<arguments>
{
  "query": "aspirin",
  "format": "JSON"
}
</arguments>
</use_mcp_tool>

download_structure

Download the structure file of a compound.

Parameters:

• cid (required): PubChem CID.
• format (optional): File format - "sdf" (default), "mol", or "smi".
• filename (optional): Customize the file name for the downloaded structure.

Example Usage:

<use_mcp_tool>
<server_name>pubchem</server_name>
<tool_name>download_structure</tool_name>
<arguments>
{
  "cid": "2244",
  "format": "sdf"
}
</arguments>
</use_mcp_tool>

Project Structure

PubChemMCP
├── pubchem_mcp_server/
│   ├── __init__.py
│   ├── server.py
│   └── tools/
│       ├── get_pubchem_data.py
│       └── download_structure.py
└── README.md

Cache Mechanism

• Data is cached after access to improve the speed of subsequent queries.
• The default cache time is 24 hours.

🔧 Technical Details

Requirements

• Python 3.8+
• Requests library
• RDKit (optional, for enhanced 3D structure handling)

📄 License

This project is licensed under the MIT License.