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PubChem

NIH chemical database — compound lookup, properties, and structure search via PUG-REST.

Manual setup 9 tools

Overview

Query chemical structures and bioactivity data from PubChem — the NIH open database of compounds, properties, synonyms, and assay summaries. No personal PubChem account or API key is required.

Prerequisites

  • A stackgate.ai account

Getting credentials

  1. Open Integrations → PubChem.
  2. Click Activate — no PubChem API key is needed.

stackgate.ai identifies itself to PubChem with a hub User-Agent per NCBI fair-use policy. For heavy research use, you may optionally store a contact email in your integration credentials so requests use your own identifier.

Using with AI clients

  • Dedicated endpoint: POST /mcp/pubchem
  • Private gateway: pubchem__* tools

Typical workflow: resolve a compound name to CID → fetch properties → read description/synonyms → search similar structures.

Troubleshooting

  • Hub quota exceeded (429) — daily fair-use limits apply on the shared hub identity. Wait until tomorrow or add an optional contact email to your integration credentials.
  • PubChem server busy (503) — PubChem throttles shared servers during high load. Retry later and reduce request frequency (max 5 requests per second).
  • Request timeout (504) — narrow structure searches (max_records) or split large workflows across multiple steps.
  • Bulk datasets — use PubChem FTP for large exports instead of repeated MCP calls.

Available tools

  • resolve_compound_by_name

    Resolve a compound name to PubChem Compound IDs (CIDs).

  • get_compound_properties

    Fetch physicochemical properties for a PubChem compound by CID.

  • get_compound_description

    Get the PubChem summary title and description for a compound CID.

  • get_compound_synonyms

    List synonyms and alternate names for a PubChem compound CID.

  • get_compound_xrefs

    Fetch cross-references (PubMed, patents, registry IDs, etc.) for a compound CID.

  • resolve_compound_by_inchikey

    Resolve a standard InChIKey to PubChem Compound IDs (CIDs).

  • search_similar_compounds

    Search PubChem for 2D structurally similar compounds using a SMILES string or CID.

  • search_substructure

    Search PubChem for compounds containing a substructure defined by SMILES or CID.

  • get_assay_summary

    Get a bioassay activity summary for a PubChem compound CID.

MCP endpoint: https://stackgate.ai/mcp/pubchem (HTTP) or via the private gateway.

Create account Documentation