MCP server

Pubchem

io.github.cyanheads/pubchem-mcp-server

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

Search PubChem compounds, properties, safety data, bioactivity, and cross-references.

Source

At a glance

Type

MCP server

Publisher

Not verified

Status

Working at last check

Tools

10

Token cost

About 7,253 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http pubchem-mcp-server https://pubchem.caseyjhand.com/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.pubchem-mcp-server]
url = "https://pubchem.caseyjhand.com/mcp"

Gemini CLI

{"mcpServers":{"pubchem-mcp-server":{"httpUrl":"https://pubchem.caseyjhand.com/mcp"}}}

Cursor

{"mcpServers":{"pubchem-mcp-server":{"url":"https://pubchem.caseyjhand.com/mcp"}}}

VS Code

{"servers":{"pubchem-mcp-server":{"type":"http","url":"https://pubchem.caseyjhand.com/mcp"}}}

Antigravity

agy mcp add pubchem-mcp-server https://pubchem.caseyjhand.com/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"pubchem-mcp-server","server_url":"https://pubchem.caseyjhand.com/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"pubchem-mcp-server","server_url":"https://pubchem.caseyjhand.com/mcp"}

Tools

• pubchem_get_bioactivity ~1028 tokens
  Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), quantitative values (IC50, EC50, Ki, etc.), each assay's type (confirmatory, screening, summary, other), and the PubMed IDs it
• pubchem_get_compound_3d_structure ~579 tokens
  Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns atoms and bonds parsed into structured fields; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lists alternate conform
• pubchem_get_compound_details ~1288 tokens
  Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacologi
• pubchem_get_compound_image ~166 tokens
  Fetch a 2D structure diagram (PNG image) for a compound by CID.
• pubchem_get_compound_interactions ~740 tokens
  Get a compound's interaction data: drug-food interactions, and the molecular targets its bioassays name — one entry per target as kinds defines it, with its assay counts by outcome and most potent active value, Active targets first, most potent first. Each entry carries its originating source. Resul
• pubchem_get_compound_safety ~312 tokens
  Get GHS (Globally Harmonized System) hazard classification and safety data for one or more compounds by CID. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes) per compound, merged across sources, plus each source's own classification — its signal wo
• pubchem_get_compound_xrefs ~768 tokens
  Get external database cross-references for a compound: PubMed citations, patent IDs, gene associations, CAS and EC numbers with the number of source records that deposited each, other registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the total count reported;
• pubchem_get_summary ~422 tokens
  Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call; identifiers past that are returned in unprocessed for a follow-up call.
• pubchem_search_assays ~466 tokens
  Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns a page of assay IDs (AIDs) — page past maxResults with offset — which can be explored further with pubchem_get_summary.
• pubchem_search_compounds ~1484 tokens
  Search PubChem for chemical compounds by identifier (name, SMILES, InChI, or InChIKey, up to 25 per call), molecular formula in Hill notation, substructure or superstructure containment, 2D Tanimoto similarity, or the compounds a bioassay (AID) found active or tested. Returns a page of CIDs — reach

Browse

• GitHub tools
• GitHub and code hosting
• Databases
• Research papers
• Health and medicine

Related MCP servers

• Pubchem
  PubChem MCP — NIH chemistry compound database (no auth)
• Mychem
  MyChem.info MCP.
• SiteCheck Health & Travel
  121 pay-per-call agent tools: health care, drug, provider and travel data tools. x402
• Biomedical Data
  Biomedical data: compounds, drug info, and molecular targets
• Inxight Drugs
  Inxight Drugs — NCATS drug development status by indication.
• Chembl
  Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.
• Rhea
  Rhea MCP — expert-curated database of biochemical reactions.
• Tariffmonkee
  Content, research, trust checks. Taiwan-specific: work permits, tax, property, fraud, localization.

Badge for your README

[![AptLynx](https://aptlynx.net/badge/io.github.cyanheads/pubchem-mcp-server.svg)](https://aptlynx.net/servers/io.github.cyanheads/pubchem-mcp-server)

Listing text is written by the maker; AptLynx lists tools and does not vouch for them. Find another tool · Browse by topic · For agents