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Chemical Compound Summary by PDB Ligand Code: Formula, Weight, InChI, SMILES (PDBe-KB)

pdbekbgraph/compound-summary

For one PDB chemical-component code (1 to 5 letters or digits, for example ATP or HEM), the compound's name, molecular formula, weight, charge, type, InChI and InChI key, SMILES, systematic names, stereoisomers, cross-links to other databases and the first PDB entry that observed it. PDBe-KB data (CC BY 4.0), passed through unmodified and served by Eden Engine; not an official PDBe or EMBL-EBI product.

activeper callv1

Price

$0.0026 per call

You pay the price shown. If a call turns out to cost more than its quote, you pay the actual price, capped at twice the quote. No monthly minimum. Top-ups start at $0.50.

Data source

Protein Data Bank in Europe (PDBe), EMBL-EBI

Data from PDBe-KB, the knowledge base of the Protein Data Bank in Europe (EMBL-EBI), published under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/); cite PDBe-KB per https://www.ebi.ac.uk/pdbe/pdbe-kb/. Served by Eden Engine; not an official PDBe or EMBL-EBI product.

Use it

Five steps: search, inspect, learn, run, settle. No per-tool setup; your agent reaches this tool through the meta-tools it already has.

Connect once and your AI can find and run this tool, and any other it needs.

Install itCreate an account
agent
// 1. search: find the tool
omnial_search({ query: "what you need" })

// 2. inspect: price and input schema
omnial_inspect({ tool: "pdbekbgraph/compound-summary" })

// 3. learn: read the usage guide at runtime
omnial_learn({ tool: "pdbekbgraph/compound-summary" })

// 4. run: price the exact call first, then run it
omnial_execute({ tool: "pdbekbgraph/compound-summary", input: { /* see input_schema */ }, dry_run: true })
omnial_execute({ tool: "pdbekbgraph/compound-summary", input: { /* ... */ } })

// 5. settle: the call is charged when it finishes, nothing to do

Not connected yet? Point your MCP client at https://mcp.eden-engine.com/mcp, then copy a config for your client.

Pricing

Every charge this tool can incur.

ChargePrice
Per call
$0.0026
Updated
Oct 21, 2026

Input and output schemas

Input schema
input_schema.json
{
  "type": "object",
  "required": [
    "compound_id"
  ],
  "properties": {
    "compound_id": {
      "type": "string",
      "pattern": "^[A-Z0-9]{1,5}$",
      "description": "PDB chemical-component (ligand) code, uppercase, 1 to 5 characters, for example ATP, HEM or NAG."
    }
  },
  "additionalProperties": false
}
Output schema
output_schema.json
{
  "type": "object",
  "description": "Keyed by the compound code; the value is a list with one compound record (`name`, `formula`, `weight`, `inchi`, `inchi_key`, `smiles`, `cross_links`, `first_observed_in`, ...).",
  "additionalProperties": true
}