Chemical Structure Search

Draw a molecule or paste SMILES, then search 580,000+ research chemicals by exact match, substructure, or similarity.

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SMILES * Paste from ChemDraw, RDKit, or any external tool. SMARTS patterns are accepted in substructure mode.

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How structure search works

Text search finds chemicals by name, CAS number, or item number — but chemists often start from a structure. This tool searches the full Aladdin catalog of more than 580,000 research chemicals directly by molecular structure, using the same open-source RDKit chemistry engine trusted across the pharmaceutical industry. Draw in the built-in editor or paste a SMILES string from ChemDraw, then choose one of three search modes.

Exact search

Finds the identical molecule in the catalog. Use it when you know precisely which compound you need and want its item number, Certificate of Analysis, and Safety Data Sheet in one step.

Substructure search

Finds every compound containing your drawn fragment — ideal for locating building blocks that share a scaffold, functional group, or core ring system. SMARTS patterns are supported for advanced queries.

Similarity search

Ranks the catalog by Tanimoto similarity on Morgan fingerprints. Lower the threshold to broaden the search — useful for finding analogs, alternatives to out-of-stock items, or inspiration in SAR exploration.

Search by structure in four steps

Draw the molecule in the editor, or paste a SMILES string from ChemDraw or RDKit.
Choose a mode: Exact for a known compound, Substructure for everything containing a fragment, Similarity for analogs.
For similarity, adjust the Tanimoto threshold — lower is broader; 0.7 is a good default.
Open any result for the product page, SDS, and COA.

Frequently asked questions

What is SMILES notation?

SMILES (Simplified Molecular Input Line Entry System) is a compact text representation of a chemical structure. For example, aspirin is written CC(=O)Oc1ccccc1C(=O)O. Most chemistry software, including ChemDraw and RDKit, can copy structures as SMILES.

What is the difference between substructure and similarity search?

Substructure search returns every compound that contains your drawn fragment as an exact subgraph — useful for finding building blocks sharing a scaffold. Similarity search instead ranks the whole catalog by Tanimoto similarity of Morgan fingerprints, returning near-matches even when no exact substructure relationship exists.

Can I use SMARTS patterns?

Yes. In substructure mode the query field accepts SMARTS as well as SMILES, so advanced users can specify wildcards, ring-membership constraints, and atom properties.

How many compounds can I search?

The structure search covers the full Aladdin Scientific catalog of more than 580,000 research chemicals, and the index is updated as new products are added.

How do I get the SDS or COA for a compound I find?

Every result card links directly to the product page, its Safety Data Sheet, and its Certificate of Analysis lookup — no separate search needed.

Need a document instead? Search SDS, COA or COO by item number. · Last updated: July 2026