PDBj Chemie

Searching

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)
• Molecular name
• Formula
• SMILES representation
• InChI representation

Notes:

• 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.

Search results

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:

Exploring

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.

See also Chemical Component Dictionary at wwPDB site for details about Chemical Component Dictionary.