// SCAN REPORT

PubChem MCP Server

30 tools. 0 can modify or destroy data without limits.

Read-only server. Low risk, but rate limits prevent runaway API costs.

Last updated: 4 Jul 2026

0 can modify or destroy data

30 read-only

30 tools total

Community server · catalogue entry verified 04/07/2026

How to control PubChem MCP Server ↓

TOOL MAP

What PubChem MCP Server exposes to your agents

Read (30) Write / Execute (0) Destructive / Financial (0)

Running more than one server? Check your whole stack →

THE RISK

What can go wrong

Even read-only tools carry cost. An agent in a retry loop can make thousands of API calls per minute, exhausting rate limits and running up bills.

POLICY

How to control PubChem MCP Server

PolicyLayer is an MCP gateway — it sits between your AI agents and PubChem MCP Server, and nothing reaches the server without passing your rules. These are the rules we recommend:

Cap read operations

{
  "analyze_molecular_complexity": {
    "limits": [
      {
        "counter": "analyze_molecular_complexity_per_minute",
        "window": "minute",
        "max": 60,
        "scope": "grant"
      }
    ]
  }
}

Controls API costs and prevents retry loops from exhausting upstream rate limits.

Create a free account and register PubChem MCP Server — nothing to install.
Add these rules — paste them, or build them visually. Tune the limits to your setup.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

ENFORCE POLICY ON PUBCHEM →

Instant setup, no code required.

FULL CATALOGUE

All 30 PubChem MCP Server tools

READ 30 tools

Read analyze_molecular_complexity Analyze molecular complexity and synthetic accessibility Read analyze_stereochemistry Analyze stereochemistry, chirality, and isomer information Read assess_drug_likeness Assess drug-likeness using Lipinski Rule of Five, Veber rules, and PAINS filters Read assess_environmental_fate Assess environmental fate including biodegradation and bioaccumulation Read batch_compound_lookup Process multiple compound IDs efficiently Read calculate_descriptors Calculate comprehensive molecular descriptors and fingerprints Read compare_activity_profiles Compare bioactivity profiles across multiple compounds Read get_3d_conformers Get 3D conformer data and structural information Read get_assay_info Get detailed information for a specific bioassay by AID Read get_compound_bioactivities Get all bioassay results and activities for a compound Read get_compound_info Get detailed information for a specific compound by PubChem CID Read get_compound_properties Get molecular properties (MW, logP, TPSA, etc.) Read get_compound_synonyms Get all names and synonyms for a compound Read get_external_references Get links to external databases (ChEMBL, DrugBank, KEGG, etc.) Read get_literature_references Get PubMed citations and scientific literature references Read get_pharmacophore_features Get pharmacophore features and binding site information Read get_regulatory_info Get regulatory information from FDA, EPA, and international agencies Read get_safety_data Get GHS hazard classifications and safety information Read get_toxicity_info Get toxicity data including LD50, carcinogenicity, and mutagenicity Read predict_admet_properties Predict ADMET properties (Absorption, Distribution, Metabolism, Excretion, Toxicity) Read search_bioassays Search for biological assays by target, description, or source Read search_by_cas_number Search for compounds by CAS Registry Number Read search_by_inchi Search for compounds by InChI or InChI key Read search_by_smiles Search for compounds by SMILES string (exact match) Read search_by_target Find compounds tested against a specific biological target Read search_compounds Search PubChem database for compounds by name, CAS number, formula, or identifier Read search_patents Search for chemical patents and intellectual property information Read search_similar_compounds Find chemically similar compounds using Tanimoto similarity Read substructure_search Find compounds containing a specific substructure Read superstructure_search Find larger compounds that contain the query structure

FAQ

Questions about PubChem MCP Server

Is the PubChem MCP Server MCP server safe to use without restrictions? +

The PubChem MCP Server server is primarily read-only with 30 read tools. While it cannot modify data, an agent in a retry loop can make thousands of API calls per minute, exhausting rate limits and running up costs. Rate limiting is still recommended.

How many tools does the PubChem MCP Server MCP server expose? +

30 tools across 1 categories: Read. 30 are read-only. 0 can modify, create, or delete data.

How do I enforce a policy on PubChem MCP Server? +

Register the PubChem MCP Server MCP server in PolicyLayer, apply the suggested rules above (adjust the limits to your use case), and point your AI client at the PolicyLayer proxy URL instead of the server directly. Your agents keep the same tools; PolicyLayer evaluates every call against policy before it executes. Nothing to install, live in minutes.

Enforce policy on every PubChem MCP Server tool call.

Deterministic rules across all 30 PubChem MCP Server tools. Per-identity grants. Full audit log. Live in minutes. Nothing to install.

ENFORCE POLICY ON PUBCHEM →

Instant setup, no code required.

30 PubChem MCP Server tools catalogued and risk-classified — across an index of 43,000+ MCP servers.