The PDBj Chemie service provides additional insights to non-protein and non-nucleotide compounds found in PDB entries. These compounds can be
searched using the PDBj Chemie Search service:
Here you can search via the following fields:
Quick search (search all fields and other meta data)
Code (three character code of an entry)
By adding the wildcard character "*" to a quick search query, partial text matches can also be found. E.g. searching for "pyridinyl*"
will return all results starting with pyridinyl.
When searching by molecular name, a wildcard search is automatically performed.
When searching via the SMILES field, the system will do a specialized search by converting the SMILES representation to a chemical fingerprint to search for exact
and partial matches. To alternatively search in a full text manner, enter the query in the "Quick search" field and prepend "@smiles".
InChI representation will always be searched in a full text manner.
When searching via the search bar in the page header, by default a quick search is performed against the ligand database.
Results are shown with a similar layout to the Mine PDB search:
Selecting an entry in the results will display the additional information (with a similar layout to the Mine PDB entries):
Each entry has three tabs:
The first tab lists the summary of the entry with its descriptors.
The second tab lists the geometry data of the entry (bond lengths, angles & torsions).
The third tab lists all PDB entries which contain this ligand entry.
The right side menu contains a 2D depiction of the molecule (SVG format) and an interactive 3D depiction using Molmil.
Clicking on the "+" icon will open the 2D/3D images in a larger, separate window.