drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/zinc.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
ZINC Database API		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/zinc.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

ZINC Database API

Base URL

https://zinc.docking.org

Auth

No API key required. Fully open public API.

URL Pattern

Resources follow a uniform pattern with format specified by file extension:

/{resource}.{format}
/{resource}/{id}.{format}
/{resource}/subsets/{subset}.{format}

Supported formats: .json, .csv, .txt, .smi, .sdf, .mol2, .xml, .png

Field selection (return only specific fields):

/{resource}.json:field1+field2+field3

Key Endpoints

Substance lookup by ZINC ID

GET /substances/ZINC000000000053.json

Search by name

GET /substances.json?preferred_name=aspirin

Search by InChIKey

GET /substances.json?inchikey=BSYNRYMUTXBXSQ-UHFFFAOYSA-N

Search by molecular formula

GET /substances.json?mol_formula=C9H8O4

Substructure search (SMILES)

GET /substances.json?sub_id-matches=c1ccccc1&count=10

Substructure search (SMARTS)

GET /substances.json?sub_id-matches-sma=[ND1]&count=10

Similarity search (Tanimoto, ECFP4 fingerprints)

The threshold (e.g., 40 = 40%) is part of the parameter name. Value can be SMILES or a ZINC ID number.

GET /substances/?ecfp4_fp-tanimoto-40=c1ccccc1O
GET /substances/?ecfp4_fp-tanimoto-70=ZINC000000000053

Browse subsets

Filter by purchasability, drug status, reactivity, or origin:

GET /substances/subsets/fda.json              # FDA-approved drugs
GET /substances/subsets/in-stock.json         # In-stock compounds
GET /substances/subsets/metabolites.json      # Metabolites
GET /substances/subsets/fda+in-stock.json     # Combine subsets with +

Key subsets:

• Purchasability: in-stock, on-demand, for-sale, bb (building blocks)
• Drug status: fda, world, in-trials, in-man, in-vivo, in-vitro
• Origin: biogenic, metabolites, natural-products, endogenous
• Reactivity: anodyne, clean, standard, reactive

Substances for a gene target

GET /genes/ACHE/substances.json?count=10

Catalogs

GET /catalogs.json                            # List all vendor catalogs
GET /catalogs/cmcd/substances.json            # Substances in a catalog

2D structure image (300x300 PNG)

GET /substances/ZINC000000000053.png

Molecule format conversion

GET /apps/mol/convert?from=CC(=O)Oc1ccccc1C(=O)O&to=inchikey

Returns the InChIKey as plain text. Supports conversions between SMILES, InChI, and InChIKey.

Batch resolution (POST)

Resolve multiple names, ZINC IDs, or SMILES at once:

POST /substances/resolved/
Content-Type: application/x-www-form-urlencoded

paste=aspirin%0Aibuprofen%0AZINC000000000053&identifiers=y&structures=y&names=y&output_format=json

Query Parameters

Pagination

• count=N — results per page (use count=all cautiously on large sets)
• page=N — page number (1-indexed)

Sorting

• sort=mwt — ascending by field
• sort=-mwt — descending (prefix with -)
• sort=no — disable sorting for faster bulk queries

Property filters (comparison operators)

• mwt-le=500 — molecular weight <= 500
• logp-ge=2 — LogP >= 2
• hbd-le=5 — H-bond donors <= 5
• Operators: -le (<=), -ge (>=), -lt (<), -gt (>), -eq (=)

Searchable substance attributes

Molecular properties: mwt, logp, hba, hbd, tpsa, rb (rotatable bonds), num_rings, num_aromatic_rings, num_heavy_atoms, num_chiral_centers, fractioncsp3

Identifiers: zinc_id, smiles, inchikey, mol_formula, preferred_name, cas_numbers

Status: purchasable, reactive, bb (building block)

Example Calls

Get properties for a compound

GET /substances/ZINC000000000053.json:zinc_id+smiles+mwt+logp+hba+hbd+tpsa+mol_formula+preferred_name

FDA drugs sorted by molecular weight

GET /substances/subsets/fda.json:zinc_id+preferred_name+mwt?sort=mwt&count=10

Drug-like compounds (Lipinski filters)

GET /substances/subsets/for-sale.json?mwt-le=500&logp-le=5&hbd-le=5&hba-le=10&count=20

Find compounds targeting a specific gene

GET /genes/EGFR/substances.json:zinc_id+preferred_name+smiles?count=10

Response Format

[
  {
    "zinc_id": "ZINC000000000053",
    "smiles": "CC(=O)Oc1ccccc1C(=O)O",
    "preferred_name": "aspirin",
    "mwt": 180.159,
    "logp": 1.31,
    "hba": 3,
    "hbd": 1,
    "tpsa": 63,
    "mol_formula": "C9H8O4",
    "inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
    "purchasable": 5
  }
]

Responses are JSON arrays. Single-record lookups (by ZINC ID) return a JSON object.

Rate Limits

No documented rate limits. The API is publicly funded (NIH NIGMS GM71896). Be respectful:

• Use count= to limit result sizes
• Use sort=no for faster bulk queries
• Similarity and substructure searches are computationally expensive — expect slower responses
• Avoid count=all on large result sets

Special Notes

• ZINC contains 2+ billion commercially available compounds — always use count= to limit results
• ZINC IDs have the format ZINC000000000053 (15-digit zero-padded after "ZINC")
• The .smi format returns SMILES strings, useful for cheminformatics pipelines
• The .sdf format returns 3D structures suitable for docking software
• Subsets can be combined with + (e.g., fda+in-stock = FDA-approved AND in-stock)
• For virtual screening workflows, use tranches (/tranches/) to partition by molecular weight and LogP