Drop a PDB or mmCIF file, or fetch an entry by its code. Everything runs in this tab.
Bridges are found from the geometry — disulfide, lactam, thioether, lactone or head-to-tail. Declare one by hand if the model does not show it closed.
Pocket2D draws a protein–ligand binding site as a 2D interaction diagram.
Give it a PDB or mmCIF file, or a PDB code: it draws the ligand, the residues around it and every contact.
A 3D view sits beside it. Save as SVG, PNG, zip or session.
It runs in your browser tab; nothing is uploaded elsewhere.
Free, with no account.
Contacts are judged from coordinates alone (hydrogen bonds without angles, bond orders sometimes inferred): not proof of binding or affinity, and distances on the paper are not the structure’s.
No. Structures stay in this tab. Sent: anonymous visit counts (a request to this site, no cookie or identifier) and, when an entry is fetched by code, including from a link or session naming one, or from #random (drawn here), that PDB code to RCSB. About 24 MB loads once.
PDB or mmCIF files (Boltz output works) and public PDB codes: four characters, a digit first (9PE1). Over 80 MB is refused; very large assemblies open slowly or not at all.
Put the code after #: https://pocket2d.com/#pdb=1IEP. Add &ligand= for the ligand, &view=3d or &view=2d for a view. Nothing after # is sent to a server; the page then asks RCSB for the entry. #random opens one drawn at random.
Cite the web address: https://pocket2d.com/