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Draw or paste a fragment to find matching records in the RDKit-parsed, formula-checked structure corpus, using molecular connectivity rather than text.
Find compounds that contain this fragment. Accepts SMILES or SMARTS.
Try an example
Your fragment becomes a query graph. RDKit checks whether it embeds inside each compound’s real bond network — so c1ccccc1 finds every benzene ring, not every "C6H6".
Each molecule is hashed into a Morgan (ECFP) fingerprint. Tanimoto similarity ranks the library by how many structural features it shares with your query.
Before a structure can be searched, RDKit-derived element counts must match its independently sourced molecular formula. This check does not establish experimental identity or scientific validation.
Common SMILES / SMARTS queries you can paste into the search box
c1ccccc1Aromatic (benzene) ring[OX2H]Hydroxyl group (alcohols, phenols, acids)[CX3](=O)[OX2H1]Carboxylic acid[CX3]=[OX1]Carbonyl (aldehydes, ketones, acids)[NX3;H2]Primary amine[CX3H1]=OAldehydeC(=O)OEster / carboxyl groupC#NNitrileSubstructure search returns compounds that strictly contain your fragment as a subgraph. Similarity search returns compounds that are structurally close overall, ranked by Tanimoto similarity of their fingerprints — useful when there is no exact fragment in common.
A formula like C6H6 tells you the atom counts, not how the atoms are bonded. Substructure matching needs connectivity, which is why this tool searches a curated, formula-checked SMILES corpus rather than the full formula database.
No. You can draw a structure or paste a plain SMILES (e.g. c1ccccc1 for benzene). SMARTS just gives you finer control over functional-group queries like [OX2H] for any hydroxyl group.
At build time, RDKit computes each SMILES element composition and it must match the compound’s independently sourced molecular formula, or the test fails. This is a formula-consistency check, not experimental structure validation.