Pubchem MCP Server

Name: Pubchem MCP Server
Author: cyanheads

by cyanheadsversion 0.8.0i★ –iComputer or cloud

Registry nameio.github.cyanheads/pubchem-mcp-server

Install

Overview

Description from the maker (original English)

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

PopNx MCP’s three pillars

These three are never merged into one score: opinions, measurements and popularity are different things.

User voiceiNo reviews yetReviews open together with accounts in a later step
Our basic checksi3 of 3 passedChecked from public information; code not scanned yet
UsageiVery new↓ 310/wk · ★ –

What you can do with it

We have not written a plain-language summary for this one yet. Below are the facts we read from the registry.

Connection: Computer or cloud
Transport: stdio, Streamable HTTP
Category: Search & AI memory

Install

Pick the AI app you use, then copy the settings.

Before you install

Basic checks: 3 of 3 passed
Runs on the maker’s server: what you ask it goes through their server.
Can do 10 things (tools) pubchem_search_compounds, pubchem_get_compound_details, pubchem_get_compound_image, pubchem_get_compound_3d_structure …
You fill in yourself: MCP_LOG_LEVEL

You need

Runs in the cloudNothing to install; it connects over the internet
npmNode.js installed (for the npx command)

Which app do you use?

ClaudeClaude CodeCursorVS CodeChatGPT

Pick your app above. We remember it, so next time the button says “Install in …”.

Works in Claude on the web, desktop and mobile:

Open Settings → Connectors
Press Add custom connector
Paste the address below and press Add
If it asks you to sign in, sign in with the maker

https://pubchem.caseyjhand.com/mcp

Or run it on your computer

Open Claude Desktop → Settings → Developer → Edit Config, and paste this into claude_desktop_config.json

{
  "mcpServers": {
    "pubchem": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "your-value"
      }
    }
  }
}

Run this in your terminal

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

Or run it on your computer

claude mcp add pubchem --env MCP_LOG_LEVEL=your-value -- npx -y @cyanheads/pubchem-mcp-server

Fill in the empty values before running it.

Open in Cursor

Or copy the settings yourself

Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json

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

Or run it on your computer

Open in Cursor

Or copy the settings yourself

Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json

{
  "mcpServers": {
    "pubchem": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "your-value"
      }
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

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

Or run it on your computer

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

{
  "servers": {
    "pubchem": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "your-value"
      }
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

ChatGPT connects only to servers on the internet:

Open ChatGPT on the web → Settings → Connectors (Apps)
Press Create or Add (some plans need Developer mode under Advanced first)
Paste the address below, give it a name and save
If it asks you to sign in, sign in with the maker

https://pubchem.caseyjhand.com/mcp

Menu names can differ slightly by plan and over time.

Your choice stays on this device in a cookie; no account needed.

Values you fill in

MCP_LOG_LEVEL env
Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').

These settings are generated from the maker’s registry entry. If the README says otherwise, follow the README.

What it can do

Tool names and descriptions exactly as the server reported them on Nov 7, 2026. The maker wrote them, not us; we show them as plain text.

pubchem_search_compounds
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 p
pubchem_get_compound_details
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),
pubchem_get_compound_image
Fetch a 2D structure diagram (PNG image) for a compound by CID.
pubchem_get_compound_3d_structure
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 lis
pubchem_get_compound_xrefs
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 t
pubchem_get_compound_safety
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 classifica
pubchem_get_bioactivity
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), a
pubchem_get_compound_interactions
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 origi
pubchem_search_assays
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_get_summary
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.

Basic checksi

We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 9, 2026

✓ Pass
Maker matches the repo
The registry name was verified with the GitHub account cyanheads, which owns the repo
… Not checked yet
Still maintained
We have not read this repo from GitHub yet
… Not checked yet
Has a licence
We have not read this repo from GitHub yet
✓ Pass
Endpoint responds
Responded in 223 ms (HTTP 200)
– Not applicable
Sign-in with OAuth
No sign-in needed
✓ Pass
No hidden instructions in tool descriptions
Read 10 tool descriptions and found no hidden instructions to the AI

Compared with others in Search & AI memoryi

More stars than 0% of the other 5763 servers in this category
Published to the registry more recently than 76% of the other 5763 servers in this category
Basic checks equal to or better than 100% of the other 5763 servers in this category

Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.

Common questions

Is Pubchem MCP Server safe?

It passed 3 of 3 applicable basic checks. We have not read the code. Before adding a key or token, see what access the server asks for and use a key with only the permissions you need.

What keys or codes does it need?

The registry does not list a required key, though some servers ask you to sign in on first use.

Does it run on my computer or in the cloud?

Either way works: install it on your computer or connect to the cloud version.

Is it still maintained?

The GitHub repo last changed –, and the latest version (0.8.0) reached the registry 12 days ago.

Which apps can use it?

Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. It connects by URL, so apps that accept remote MCP servers work too, such as ChatGPT in developer mode.

What can I use instead?

In the same category: Context7, Codebase Memory, Exa

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README from the maker

Open the README

Copied from the maker’s repo as written. PopNx MCP has not reviewed or endorsed it. HTML, images and scripts are removed. Links lead off this site.

@cyanheads/pubchem-mcp-server Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP. 10 Tools • 6 Resources • 1 Skill

Public Hosted Server: https://pubchem.caseyjhand.com/mcp

Overview

Chemical compounds and bioassays from PubChem. Search compounds by name, formula, or structure; fetch properties, safety data, bioactivity, drug-food interactions, molecular targets, and 3D structures; and find bioassays by biological target.

Tools

Tool	Description
`pubchem_search_compounds`	Search for compounds by name, SMILES, InChI, InChIKey, formula, substructure, superstructure, or 2D similarity, or list the compounds a bioassay found active.
`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_3d_structure`	Fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF.
`pubchem_get_compound_xrefs`	Get external database cross-references (PubMed, patents, genes, CAS and EC numbers, etc.).
`pubchem_get_compound_safety`	Get GHS hazard classification and safety data for one or more compounds by CID (batch).
`pubchem_get_bioactivity`	Get a compound's bioactivity profile: assay results, targets, activity values, assay types, and cited PubMed IDs; filter by outcome, molecular target, or assay type.
`pubchem_get_compound_interactions`	Get a compound's drug-food interactions and the molecular targets its assays name, each with assay counts and the most potent active value.
`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.

Resources

Compound and assay records are also exposed as URI-templated resources, backed by the same client methods as the tools; many MCP clients are tool-only and never surface resources.

Resource	Description
`pubchem://compound/{cid}`	Core physicochemical properties (JSON).
`pubchem://compound/{cid}/safety`	GHS hazard classification (JSON).
`pubchem://compound/{cid}/image`	2D structure diagram (PNG).
`pubchem://compound/{cid}/xrefs`	External cross-references (JSON).
`pubchem://compound/{cid}/bioactivity`	Bioassay activity profile (JSON).
`pubchem://assay/{aid}`	BioAssay summary (JSON).

Skills

The server publishes an agent skill, pubchem-guide, covering gates and identifier chains the tool descriptions don't carry: salt vs parent CIDs, where Gene IDs and accessions come from, why gene-symbol, Gene ID, and accession searches disagree, and how to read activity labels, potency values, and GHS data. Plugin installs (Claude Code, Codex) and the .mcpb bundle pick it up from skills/, and the server also serves it over MCP as skill://pubchem-guide/SKILL.md.

Capability reference

`pubchem_search_compounds` tool

Six search strategies: identifier (identifierType + identifiers; name/SMILES/InChI/InChIKey, 25 per call, the rest returned in unprocessed), formula (formula, Hill notation, optional allowOtherElements), substructure/superstructure and 2D similarity (query + queryType; similarity threshold 70-100, default 90), or assay (aid; compounds the bioassay marked active, or every compound tested with activeOnly: false)
Up to 200 CIDs per page (default 20; a larger maxResults is served at 200 and reported in cappedInputs); offset pages identifier and assay searches to the end of their matches, and formula, substructure, superstructure, and similarity searches to 10,000 (deeper fails with offset_ceiling_exceeded). Optional properties saves a follow-up pubchem_get_compound_details call
Reports totalFound, or a totalFoundAtLeast floor when an upstream search saturated, and unresolvedIdentifiers for inputs with no CID. Fails with aid_not_found for an unknown AID and search_query_rejected (with a hint) for a query PubChem cannot search

`pubchem_get_compound_details` tool

Up to 100 CIDs per call (the rest returned in unprocessed); 27 available properties, defaulting to a core set of 14
Optional descriptions (descriptionOffset/maxDescriptions, default 3, max 20) and classification (FDA, MeSH, ATC) cover the first 10 CIDs only, the rest listed in skippedCids. Optional synonyms (synonymOffset/maxSynonyms, default 20, max 100) and a Lipinski/Veber drug-likeness check cover every found CID
Per-CID found: false separates a nonexistent CID from a compound with no data

`pubchem_get_compound_image` tool

Single CID; size is "small" (100x100) or "large" (300x300, default)
Returns base64-encoded PNG plus width/height
Typed cid_not_found error when PubChem has no record for the CID

`pubchem_get_compound_3d_structure` tool

Single CID; format="json" (default) returns parsed atoms (element + x/y/z) and bonds, format="sdf" returns the raw V2000 SDF text
maxAtoms/maxBonds cap the JSON preview (default 200 each); atomCount/bondCount always report the full totals, with any capping disclosed via enrichment
includeRawSdf bypasses the default 500-line cap on the raw SDF text
Optional includeAlternateConformerIds lists conformer IDs beyond the default
Typed no_3d_structure error when PubChem has no computed 3D coordinates (large molecules, mixtures, some salts)

`pubchem_get_compound_xrefs` tool

Single CID; one or more xrefTypes: CAS, EC, RN, RegistryID, PatentID, PubMedID, GeneID, ProteinGI, TaxonomyID
CAS and EC are the numbers deposited for the compound, every distinct value ordered by how many source records deposited it, with those counts in sourceCounts. RN is PubChem's unranked registry-number list: the CAS number sits beside deprecated and related CAS RNs and EC numbers
ProteinGI currently returns no data from PubChem; use GeneID for gene/protein associations
maxPerType up to 500 (default 50), with one offset applied to every type; each type reports totalAvailable and truncated. PubMedID comes newest first
A type that fails to load is named in failedTypes and the others still return; the call fails only when a type fails and no type other than ProteinGI (which PubChem no longer serves) loads. An empty result says whether the compound has none of the requested types or the CID may be mistyped

`pubchem_get_compound_safety` tool

Up to 25 CIDs per call (the rest returned in unprocessed)
Returns the GHS signal word, pictograms, H-codes, and P-codes merged across sources, plus classifications[] with each source's own label; precautionary statements carry a decoded flag
Per-CID status: ok, not_classified (notifiers found no GHS hazard), no_ghs_data (no deposited classification), or cid_not_found, so a bad CID never reads as "no hazards on file"

`pubchem_get_bioactivity` tool

Single CID; filter by outcomeFilter (active/inactive/all, default all), targetGeneId/targetAccession, and assayType (any of confirmatory/screening/summary/other); an assay must pass every filter set
A target filter matches any identifier tied to the same target, so Gene ID 5742, UniProt P23219, and RefSeq NP_542158 all reach the same COX-1 assays
Each result carries the assay's assayType and the PubMed IDs it cites (pmids, newest first)
Up to 100 results per page (default 20); offset reaches the rest. A multi-target assay reports the matched target and lists the others under otherTargets
Reports totalAssays/activeCount/inactiveCount for the whole compound and filteredCount/returnedCount for the page; notices say whether there is no data, the filter excluded everything, or offset is past the end

`pubchem_get_compound_interactions` tool

Single CID; one or more kinds — drug-food (PUG View), target, drug-drug (DrugBank); default ["drug-food"], and an empty drug-food page points at target
target gives one entry per target the compound's assay summary names: a Gene ID with the accessions the table pairs with it, or an identifier it never pairs. A Gene ID and an accession that no row pairs are separate entries even when they name the same protein (erlotinib's ERBB2 appears as accession:P04626 and as GeneID:2064). Each entry names the target from a batched gene or protein summary lookup, plus the GeneID: or accession: value pubchem_get_bioactivity filters on, and states the assay counts by outcome and the most potent Active value with its AID. Active targets come first, most potent first. If a name lookup fails or does not answer within a few seconds, the entries keep their identifier and the notice says so
maxEntries per kind per page (max 50, default 10); offset counts records (targets, for target), up to 2,147,483,646. Each kind pages independently, reported in paging[] (totalRecords/nextOffset/truncated)
A kind that fails is named in failedKinds and the others still return. The notice offers a retry only for a failure a retry can clear (timeout, rate limit, network error, unreadable response, 5xx other than 501); an HTTP 400, 403, or 501, or a response in a shape the server does not expect, fails the same way on every call. drug-drug comes from PubChem's SDQ service, which refuses automated requests, so it lands in failedKinds and a retry will not help

Only the beginning is shown; read the rest in the repo

Pubchem MCP Server

Overview

PopNx MCP’s three pillars

What you can do with it

Install

Before you install

Or run it on your computer

Or run it on your computer

Or run it on your computer

Or run it on your computer

Values you fill in

What it can do

Basic checksi

Maker matches the repo

Still maintained

Has a licence

Endpoint responds

Sign-in with OAuth

No hidden instructions in tool descriptions

Compared with others in Search & AI memoryi

Common questions

Alternatives

Context7

Codebase Memory

Exa

README from the maker

Overview

Tools

Resources

Skills

Capability reference

pubchem_search_compounds tool

pubchem_get_compound_details tool

pubchem_get_compound_image tool

pubchem_get_compound_3d_structure tool

pubchem_get_compound_xrefs tool

pubchem_get_compound_safety tool

pubchem_get_bioactivity tool

pubchem_get_compound_interactions tool

`pubchem_search_compounds` tool

`pubchem_get_compound_details` tool

`pubchem_get_compound_image` tool

`pubchem_get_compound_3d_structure` tool

`pubchem_get_compound_xrefs` tool

`pubchem_get_compound_safety` tool

`pubchem_get_bioactivity` tool

`pubchem_get_compound_interactions` tool