MCP Servers / database / PubChem MCP Server

PubChem MCP Server

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stdionone9database

Provides comprehensive access to PubChem's chemical information database via the PubChem PUG REST API.

Install
How to run this server

No install command recorded.

server path: pubchem-mcp-server-2
Tools
What this server exposes
pubchem_search_compounds
Search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity.
pubchem_get_compound_details
Get physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID.
pubchem_get_compound_image
Fetch a 2D structure diagram (PNG) for a compound by CID.
pubchem_get_compound_safety
Get GHS hazard classification and safety data for a compound.
pubchem_get_compound_xrefs
Get external database cross-references (PubMed, patents, genes, proteins, etc.).
pubchem_get_bioactivity
Get a compound's bioactivity profile: assay results, targets, and activity values.
pubchem_search_assays
Find bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession).
pubchem_get_summary
Get summaries for PubChem entities: assays, genes, proteins, taxonomy.
Configuration
Environment & auth
authnone
envMCP_HTTP_PORT
envMCP_HTTP_HOST
Resources
PubChem MCP Server — MCP Server · libregistry