PubChem fields and properties

This page defines the PubChem fields you can return — identifiers, physicochemical properties, structural metadata, and assay links — and recommends which to include. Selecting only the fields you need is what most affects export size and reproducibility, since PubChem can return large payloads and some properties are missing for subsets of the database.

PubChem fields and properties

Choose only the fields you need to keep exports lean and reproducible.

Core identifiers

• CID: PubChem compound ID (stable).
• InChIKey / InChI: hashed and full IUPAC identifiers for exact matching.
• SMILES / IsomericSMILES: structure strings. PubChem retired the CanonicalSMILES field name in 2025 in favor of SMILES (same canonical/connectivity structure) — requesting the old name returns a null column, so the platform requests SMILES on the wire and accepts either name as input.
• IUPACName: the systematic chemical name.
• synonyms: up to 10 names (trade names, CAS numbers, common names), fetched automatically alongside properties — not gated by the properties list.

Physicochemical properties

• MolecularFormula
• MolecularWeight / MonoisotopicMass / ExactMass
• TPSA
• HBondDonorCount / HBondAcceptorCount
• RotatableBondCount
• XLogP (logP estimator; may be missing)
• Charge
• Volume3D

Structural metadata

• Complexity, HeavyAtomCount, IsotopeAtomCount, CovalentUnitCount
• Fingerprint2D
• AtomStereoCount, DefinedAtomStereoCount, UndefinedAtomStereoCount
• BondStereoCount, DefinedBondStereoCount, UndefinedBondStereoCount

Assay and links

• pubchem_url: canonical record link (https://pubchem.ncbi.nlm.nih.gov/compound/{CID}), always included — built from the CID, not requested via properties.
• Assay links come from a separate PubChem bioassay lookup, not the property lookup: ask Ivy for the bioassay data linked to a CID.

Field selection tips

• A property lookup returns the fields listed above by default — pubchem_url and up to 10 synonyms come back regardless. Name the properties you want in your request to get a narrower subset of the fields above; a name outside that set is silently dropped.
• For a lean export, request only the identifiers and properties you need — synonyms and pubchem_url add to payload size but cannot be turned off.

Data quality notes

• Some properties are missing for subsets of the database; blank fields indicate absence, not an error.
• Synonyms can contain duplicates or deprecated names; rely on InChIKey for matching.
• XLogP values may come from different estimation methods; treat as approximate.