Use Rowan's protein–ligand interaction diagram utility to:
visualize a bound pose starting from a PDB file or from any PDB ID,
analyze hydrogen bonding, polar and hydrophobic interactions, and
generate visualizations for communicating about the quality of poses.
If anything here isn't working like you expect, let us know via contact@rowansci.com. If you'd like to use structure-based drug design tools like docking, co-folding, molecular dynamics, and FEP, consider making a Rowan account.
To select a project structure, click on the row and then click "Select."
PDB ID
Name
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For best results, upload a PDB that includes hydrogens; hydrogen-bond detection expects explicit hydrogen atoms.
Load a PDB to view the structure
How it works
The diagram treats the selected ligand as the center of the binding site, then scans nearby protein residues for simple geometry-based contacts. If you provide a SMILES, RDKit is used to draw the ligand; otherwise the ligand layout is inferred from the PDB coordinates.
The input structure should include hydrogens. Hydrogen-bond detection depends on explicit donor hydrogens in the PDB.
Hydrogen bonds require a donor–hydrogen–acceptor angle of 120–180°, a donor–acceptor distance of at most 3.5 Å, and a hydrogen–acceptor distance of at most 2.7 Å.
Polar contacts are close contacts between polar heavy atoms (N, O, or S) that are not classified as hydrogen bonds.
Hydrophobic contacts are close contacts between neutral carbon-like ligand atoms (C or S) and hydrophobic side-chain atoms.
Salt bridges are detected between charged ligand atoms and nearby charged residues.
Gray residue labels show generic van der Waals contacts: close heavy-atom contacts that are not classified as hydrogen bonds, salt bridges, polar contacts, or hydrophobic contacts.
Ligand surface outlines also use nearby residues within 5 Ă…, up to 100 residues, to help show which parts of the ligand are protein-facing versus solvent-exposed.
If this interaction diagram leaves anything to be desired, we recommend checking out the following tools: