Get detailed compound information from PubChem including chemical properties, synonyms, and classifications. Search by CID, name, SMILES, InChI, or molecular formula.
AI agents call pubchem_compound to retrieve information from Entrez MCP Server without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
This tool queries a public chemical database and returns information without creating, modifying, deleting, or executing arbitrary operations. The search and retrieval operations are read-only with no capability to alter data or trigger external actions. The low severity reflects minimal risk even if misused by an AI agent—it can only retrieve publicly available chemical compound information.
From the tool's definition Tool performs 'Get detailed compound information' and 'Search' operations from PubChem. The description uses only retrieval verbs (Get, Search) with no side effects.
Attacks that exploit this kind of access
Get detailed compound information from PubChem including chemical properties, synonyms, and classifications. Search by CID, name, SMILES, InChI, or molecular formula. It is categorised as a Read tool in the Entrez MCP Server MCP Server, which means it retrieves data without modifying state.
Register the Entrez MCP Server MCP server in PolicyLayer and add a rule for pubchem_compound: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches Entrez MCP Server. Nothing to install.
pubchem_compound is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the pubchem_compound rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.
Set action: deny in the PolicyLayer policy for pubchem_compound. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.
pubchem_compound is provided by the Entrez MCP Server MCP server (leongxj123/entrez-mcp-server). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Every MCP server has a record like this.
Type a name, get the same breakdown: verified identity, auth posture, risk grade, capabilities, recommended policy.
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