ChEMBL

ChEMBL

ChEMBL is EMBL-EBI's public database of bioactive molecules and their measured activities; this connector searches it directly from inside RxCubed. It's available under Collect files. Look a compound up by name or ChEMBL ID — “acetazolamide”, for example. See File Collection for the shared search, shortlist and save flow every connector here uses.

Identifier lookup, not ranked search

Like PubChem, ChEMBL is an identifier lookup: you name a compound and get its recorded activities back, rather than browsing a ranked candidate list. There is no AI scoring, no Qualities, and no importance controls.

What to compare

Each row is one measured activity, not one compound. The card shows the molecule, the target, the assay type, the reported value, pChEMBL, and the assay description.

pChEMBL is the column to read first. It is the negative log of the reported potency in molar units, put on one scale so that different assay readouts can be compared:

• pChEMBL 9 = 1 nM — very potent;
• pChEMBL 7 = 100 nM — potent;
• pChEMBL 5 = 10 µM — weak.

Higher is more potent. Because it normalises IC50, Ki, Kd and EC50 onto one axis, it is the fairest single number for comparing rows — but read the assay description before comparing across very different assay formats.

This is measured data, and that matters

Everything ChEMBL returns was observed in an experiment and reported in a paper. That makes it a different kind of evidence from a computed property or a prediction, and much stronger. It also means the usual experimental caveats apply: different labs, different conditions, different constructs, and occasional transcription errors.

Files

• Structure (SDF) — the compound, selected by default.
• 2D depiction (SVG) — a scalable picture for reports and notes.

Papers

ChEMBL records cite the papers the measurements came from. Tick them under Papers in the shortlist before saving, or open Group ▾ on a saved row afterwards, and they are saved as literature evidence in the same group — which is how an activity value in a report can point at the paper that reported it.

What to do next

Pair a ChEMBL activity with the compound's PubChem record for computed properties, and with a structure from RCSB PDB to see where the compound binds.