Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns parsed atoms and bonds the model can reason over directly; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lists al...
Risk signalsBulk/mass operation — affects multiple targets
Part of the Pubchem server.
Free to start. No card required.
AI agents call pubchem_get_compound_3d_structure to retrieve information from Pubchem without modifying any data. This is common in research, monitoring, and reporting workflows where the agent needs context before taking action. Because read operations don't change state, they are generally safe to allow without restrictions -- but you may still want rate limits to control API costs.
Even though pubchem_get_compound_3d_structure only reads data, uncontrolled read access can leak sensitive information or rack up API costs. An agent caught in a retry loop could make thousands of calls per minute. A rate limit gives you a safety net without blocking legitimate use.
Read-only tools are safe to allow by default. No rate limit needed unless you want to control costs.
{
"version": "1",
"default": "deny",
"tools": {
"pubchem_get_compound_3d_structure": {}
}
}See the full Pubchem policy for all 10 tools.
These attack patterns abuse exactly the kind of access pubchem_get_compound_3d_structure gives an agent. Each links to the full case and the policy that stops it:
Other read tools across the catalogue. The same approach applies to each: allow, with a rate cap to control cost.
Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns parsed atoms and bonds the model can reason over directly; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lists alternate conformer IDs. Not every compound has computed 3D coordinates (large molecules, mixtures, and some salts do not).. It is categorised as a Read tool in the Pubchem MCP Server, which means it retrieves data without modifying state.
Register the Pubchem MCP server in PolicyLayer and add a rule for pubchem_get_compound_3d_structure: 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 Pubchem. Nothing to install.
pubchem_get_compound_3d_structure 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_get_compound_3d_structure 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_get_compound_3d_structure. 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_get_compound_3d_structure is provided by the Pubchem MCP server (https://pubchem.caseyjhand.com/mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Deterministic rules across all 10 Pubchem tools. Per-identity grants. Full audit log. Live in minutes. Nothing to install.
Free to start. No card required.
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