Pubchem Mcp Server

What is Pubchem Mcp Server about?

Retrieves essential drug data such as name, CAS number, molecular weight, formula, SMILES, synonyms, InChI Key, IUPAC name, ATC code and a details link directly from PubChem.

How to use Pubchem Mcp Server?

1. Clone the repository and install the package with pip install ..
2. Ensure Python 3.10 and the required dependencies (python-dotenv, requests, mcp, uvicorn) are available.
3. Configure the server in a servers_config.json file following the example provided, then launch it with uvx pubchem_mcp_server (or the appropriate command defined in the config).
4. Send requests to the MCP endpoint; the server will respond with a JSON payload containing the drug information.

Key features of Pubchem Mcp Server

• Simple installation via pip.
• Minimal dependencies, leveraging the standard PubChem REST API.
• Returns a comprehensive, ready‑to‑use JSON structure.
• Configurable through a JSON file compatible with Claude Desktop server integration.
• Supports execution with uvicorn/uvx for fast ASGI serving.

Use cases of Pubchem Mcp Server

• Building pharmaceutical knowledge bases.
• Enriching drug discovery pipelines with chemical descriptors.
• Providing quick lookup services for clinical decision support tools.
• Supplying data for cheminformatics research and education.

FAQ from the Pubchem Mcp Server

Q: Which Python version is required? A: Python 3.10.

Q: How do I add an API key if needed? A: Include it in the environment variables section of servers_config.json (e.g., "env": {"API_KEY": "<YOUR_API_KEY>"}).

Q: Can I run the server on a different port? A: Yes, pass the desired port to the underlying uvicorn command when starting the server.

Q: What format is the output? A: A JSON object with fields like Drug Name, CAS Number, Molecular Weight, etc.

pubchem mcp server

the mcp is used to extract the drug basic chemical infomation from pubchem API.

Requirements

• Python 3.10
• python-dotenv
• requests
• mcp
• uvicorn

Installation

Install the dependencies(local):

• Install directly from the project directory

git clone [project repository URL]
cd [project directory]
pip install .

Configure servers(pypi):

The servers_config.json follows the same structure as Claude Desktop, allowing for easy integration of multiple servers. Here's an example:

{
  "mcpServers": {
    "pubchem": {
      "command": "uvx",
      "args": ["pubchem_mcp_server"]
    }
  }
}

the result of this MCP

{
  "Drug Name": "Aspirin",
  "CAS Number": "50-78-2",
  "Molecular Weight": 180.16,
  "Molecular Formula": "C9H8O4",
  "SMILES": "CC(=O)OC1=CC=CC=C1C(=O)O",
  "Synonyms": [
    "2-(Acetyloxy)benzoic Acid",
    "Acetylsalicylic Acid",
    "Acetysal",
    "Acylpyrin",
    "Aloxiprimum",
    "Aspirin",
    "Colfarit",
    "Dispril",
    "Easprin"
  ],
  "InchI Key": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
  "IUPAC Name": "2-acetyloxybenzoic acid",
  "ATC Code": "N02BA01",
  "Details Link": "https://pubchem.ncbi.nlm.nih.gov/compound/2244"
}