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

pubchem_get_compound_3d_structure is exposed by the Pubchem MCP Server MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), and the pubchem_get_compound_3d_structure tool becomes available to the model automatically. See the full listing for setup details and every tool this server provides.

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.