science.pdb.ligand

Get chemical component data for a ligand/small molecule by its 3-letter PDB code — name, molecular formula, weight, type, formal charge, heavy atom count, SMILES/InChI descriptors. Covers ATP, HEM, NAG, drug molecules, cofactors, ions, and 40K+ chemical entities in the PDB (RCSB PDB)

SERVERApibase SOURCEapibase-mcp-client

Low RISK CLASS

Category Read

Parameters 11 required

Recommended Allowedsee the rule below

Registry record Grade F, identity unverified Pull the record →

This record as markdown: /tools/io-github-whiteknightonhorse-apibase/science.pdb.ligand.md

WHAT IT DOES

What science.pdb.ligand does on Apibase

AI agents call science.pdb.ligand to retrieve information from Apibase without modifying anything. It is typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.

Parameter	Type	Required	Description
`ligand_id`	string	Yes	Chemical component identifier — standard 3-letter code (e.g. "ATP" for adenosine triphosphate, "HEM" for heme, "NAG" for N-acetylglucosamine, "ZN" for zinc ion)

Parameters from the server's own tool schema.

RISK

Why science.pdb.ligand is rated Low

Retrieves chemical metadata from public PDB database; no modification, deletion, or execution.

From the tool's definition Get chemical component data for ligand by PDB code — name, formula, weight.

Attacks that exploit this kind of access

RECOMMENDED RULE

The rule that runs science.pdb.ligand safely

PolicyLayer is an MCP gateway: it sits between your AI agents and Apibase, and checks every tool call against a rule you set before the call runs. Nothing changes on the server itself. For science.pdb.ligand, this is the rule to start with:

science.pdb.ligand Allowed

science.pdb.ligand is read-only, so it stays allowed. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "science.pdb.ligand": {}
  }
}

ALLOW ONLY THIS TOOL → Instant setup, no code required.

The button opens the PolicyLayer dashboard: create your workspace, connect Apibase, apply this rule, and every science.pdb.ligand call is checked against it from then on.

FAQ

Questions about science.pdb.ligand

What does the science.pdb.ligand tool do? +

What parameters does science.pdb.ligand accept? +

science.pdb.ligand accepts 1 parameter: ligand_id. Required: ligand_id. The full parameter table on this page comes from the server's own tool schema.

How do I enforce a policy on science.pdb.ligand? +

Register the Apibase MCP server in PolicyLayer and add a rule for science.pdb.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 Apibase. Nothing to install.

What risk level is science.pdb.ligand? +

science.pdb.ligand is a Read tool with low risk. Read-only tools are generally safe to allow by default.

Can I rate-limit science.pdb.ligand? +

Yes. Add a rate_limit block to the science.pdb.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.

How do I block science.pdb.ligand completely? +

Set action: deny in the PolicyLayer policy for science.pdb.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.

What MCP server provides science.pdb.ligand? +

science.pdb.ligand is provided by the Apibase MCP server (apibase-mcp-client). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.

KEEP EXPLORING

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