pubchem_get_compound_3d_structure

MCP tool from Pubchem MCP Server by cyanheads

Fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF.

How to use it

Project documentation lists pubchem_get_compound_3d_structure for the Pubchem MCP Server MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), then check which tools your installed version makes available. Tool availability can depend on configuration and credentials. A server handshake does not verify this tool’s behavior. See the full listing for setup details.

Install Pubchem MCP Server

$docker run -p 3010:3010 pubchem-mcp-server

FULL PUBCHEM MCP SERVER LISTING

Other tools in Pubchem MCP Server (10)

maxAtoms

/maxBonds bound the atom/bond preview and includeRawSdf opts into a large raw SDF past the safe line cap; atomCount/bondCount always report the totals and any capping is disclosed

pubchem_get_bioactivity

Get a compound's bioactivity profile: assay results, targets, and activity values; filter by outcome or molecular target.

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_interactions

Get drug-drug, drug-food, and chemical-target interactions for a compound by CID.

pubchem_get_compound_safety

Get GHS hazard classification and safety data for one or more compounds by CID (batch).

pubchem_get_compound_xrefs

Get external database cross-references (PubMed, patents, genes, proteins, etc.).

pubchem_get_summary

Get summaries for PubChem entities: assays, genes, proteins, taxonomy.

pubchem_search_assays

Find bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession).

pubchem_search_compounds

Search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity.