Proteins Meet Ligands: BindingDB in the Generator
ChemIllusion now connects the small-molecule you draw with BindingDB-backed protein targets, optional AlphaFold models, and a clearer Protein Structure Viewer so medicinal chemistry and teaching workflows stay on one canvas.
Medicinal chemistry and biochemistry teaching often need the same scene: a ligand in hand, and a believable protein target next to it. Jumping between databases, structure pages, and a drawing tool breaks the story you are trying to tell.
Today's generator update closes that loop. When you have a structure on the canvas, ChemIllusion can ask BindingDB which macromolecular targets are associated with that chemotype, show affinity-style metadata when available, and route you into the Protein Structure Viewer with explicit badges for experimental PDB models versus AlphaFold predictions.
Example: acetazolamide and carbonic anhydrase
A concrete pairing many instructors already use is the sulfonamide drug acetazolamide with carbonic anhydrase. Below is the 2D structure for the SMILES string CC(=O)Nc1nnc(S(N)(=O)=O)s1 (RDKit-drawn), alongside a Cα backbone trace of human carbonic anhydrase II from PDB entry 1CA2 (experimental coordinates from the PDB archive).
Acetazolamide (SMILES drawn with RDKit).
Carbonic anhydrase II — Cα trace of PDB 1CA2 (256 Cα atoms).
How the workflow fits together
Open Add Protein Image from the left canvas toolbar. If your Ketcher selection carries a SMILES that BindingDB recognizes, you will see a compact banner with hit counts and a path into the full hit list. Choose a target, confirm the structure source (experimental PDB versus AlphaFold), load the structure into NGL, then export the rendered protein image back onto the canvas beside your ligand.
The viewer modal: load by PDB ID, pick representation (here cartoon for crambin 1CRN), optional transparent export, and Add to Canvas when you are ready.
When BindingDB has data for your ligand, a banner appears above the viewer with a quick count and a one-click path into the hit list.
What you will see in the Protein Structure Viewer
The modal pairs the interactive NGL viewport with BindingDB-driven context: target names, similarity or curated-hit confidence labels when we have them, and ligand thumbnails for quick visual confirmation. A dedicated Include AlphaFold predicted structures toggle keeps experimental PDB coordinates the default while still giving you access to high-confidence models when PDB coverage is thin.
BindingDB requests, AlphaFold enrichment when you ask for it, and quick structure previews are handled on the server with caching so the canvas stays responsive while you iterate.
Whether you are preparing a slide, a problem set, or a journal-club figure, the goal is the same: keep ligand design and protein context in one ChemIllusion workspace—and choose PDB versus AlphaFold deliberately from the badges before you export.
Walk through BindingDB targets and the protein viewer with the Drawing Coach lesson.
Open the BindingDB protein lesson in the Generator →