ligand
AI agents call ligand to retrieve information from Mcp Rcsb Pdb without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
This tool retrieves ligand data from the Protein Data Bank. Ligands are small molecules (ions, drugs, cofactors) bound to proteins, and retrieving their data is a read-only operation with no side effects. The sibling tools are all query/retrieval operations on public structural biology data. There is no indication this tool modifies, executes code, or causes destructive effects.
From the tool's definition Tool name 'ligand' on RCSB PDB server; sibling tools include 'search', 'structure', 'summary', 'assembly', 'polymer_entity' which are all retrieval/query operations. Server description states it 'retrieves experimental protein structures' and 'ligands'.
Attacks that exploit this kind of access
ligand. It is categorised as a Read tool in the Mcp Rcsb Pdb MCP Server, which means it retrieves data without modifying state.
Register the Mcp Rcsb Pdb MCP server in PolicyLayer and add a rule for ligand: 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 Mcp Rcsb Pdb. Nothing to install.
ligand 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 ligand 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 ligand. 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.
ligand is provided by the Mcp Rcsb Pdb MCP server (pipeworx-io/mcp-rcsb-pdb). 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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