PubChem MCP Server

What is PubChem MCP Server?

PubChem MCP Server is a Python implementation of a Model Context Protocol (MCP) server that allows AI models to query chemical compound information from the PubChem database. It provides easy access to compound properties, 2D structures, and 3D molecular coordinates through a standard MCP interface.

How to use PubChem MCP Server?

Install from source with pip install -e . (optionally pip install -e ".[rdkit]" for enhanced 3D handling). Configure the server in your MCP settings file by providing the path to mcp_server.py and listing the tools get_pubchem_data and download_structure under autoApprove. Then invoke the tools by passing a compound name or PubChem CID as the query parameter.

Key features of PubChem MCP Server

• Query compounds by name or PubChem CID
• Retrieve IUPAC name, molecular formula, weight, SMILES, InChI, InChIKey
• Output in JSON (default), CSV, or XYZ (3D) format
• Built-in in-memory caching for API responses
• Automatic retry mechanism for API reliability
• Fallback 3D structure generation if PubChem 3D unavailable

Use cases of PubChem MCP Server

• Query chemical compound properties directly from an AI assistant
• Retrieve standard identifiers (SMILES, InChI, InChIKey) for cheminformatics workflows
• Download structure files (SDF, MOL, SMI) for a given PubChem CID
• Obtain 3D molecular coordinates for visualization or modeling
• Integrate chemical data lookup into automated research pipelines