PubChem

PubChem

PubChem is the NIH's public database of chemical compounds and their properties; this connector searches it directly from inside RxCubed. It's available under Collect files. Look a compound up by name, CID, SMILES, or InChIKey — “acetazolamide” or “CID 1986”, for example. See File Collection for the shared search, shortlist and save flow every connector here uses.

Identifier lookup, not ranked search

PubChem is an identifier lookup: you are asking for a specific compound, not browsing candidates. It returns the matching record rather than a ranked list, so there is no AI scoring, no Qualities, and no importance controls. If a name is ambiguous, use the CID.

What to compare

The result card shows CID, molecular formula, molecular weight, XLogP, and TPSA — the two properties most often used as a first sanity check on whether a molecule is drug-like at all. Synonyms, identifiers, and the rest of PubChem's computed properties are under Details ▾.

Files

• Structure (2D SDF) — the connection table, selected by default. This is the right input for most property and filter tools.
• Structure (3D SDF) — a computed conformer. Use it when a tool needs coordinates, and remember it is one generated conformation, not a measured one.
• 2D depiction (image) — a picture for reports and notes.

What to do next

A saved 2D SDF is the usual input to drug-likeness filters and molecular properties. To generate 3D conformations properly rather than taking PubChem's single one, use conformer generation. To compare a compound against a protein structure you have collected, see contact mapper (chemical).

For measured activity against a target rather than computed properties, use ChEMBL.