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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:
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
  • 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:
PDBj Chemie Search results (for query "*", meaning wildcard, i.e. match everything)


Selecting an entry in the results will display the additional information (with a similar layout to the Mine PDB entries):
PDBj Chemie entry (for entry "000")
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.

Created: 2014-08-21 (last edited: more than 1 year ago)2015-11-06
PDB entries from 2020-09-23