Help: Ligands

The Ligand page contains 4 tabs: Summary, Family interactions, Structures and Download. Below is a brief description of each section:

Summary Back to top

The ligand summary tab contains more structured data than the family page. The table in the summary tab includes the ligand name, formula, molecular weight, InChI (IUPAC International Chemical Identifier) and SMILES (Simplified Molecular-Input Line-Entry System) string. For each ligand entry, external database cross-links are provided to both PDB RSCB and PDBe, and where possible to ChEBI and/or ChEMBL. Where possible we provide additional annotation from Wikipedia. We provide additional functional annotations for protein family entries by using the Wikipedia article mapping provided by Pfam. Linking between iPfam ligand entries and Wikipedia articles was performed by cross referencing the stored ligand InChI with the InChI found in the Wikipedia chembox or drugbox infoboxes. Initially only a summary of the Wikipedia article will be displayed. For each Wikipedia article, currently mapped via the InChI, we generate a summary for that article. You can reveal the full article by viewing the ‘full article’ in the iPfam, or by going to Wikipedia. If you want to edit this article, then use the link in the top, right of the Wikipedia summary. Note, this will change the article content at Wikipedia, not in iPfam, where it will take a day or so to be propagated through. If you know of articles that we are missing, then please email us.

Interactions Back to top

Adjacent to the summary tab is the Family interactions tab. The table on this tab lists all detected interactions between the ligand and protein families (or domains) and the number of occurrences of the interaction in the iPfam database. You can access details of the pairwise interaction by using the ‘Structures’ and ‘Sequences’ buttons in the table. Selecting either of these buttons takes you to the next level of detail in the site, see the interactions help for more info.

Structures Back to top

The Structures tab provides a table listing all PDB entries that contain the ligand. This table presents the PDB identifier, PDB title, number of times this ligand occurs, and the number of domain-ligand interactions.

Download Back to top

The Download tab offers the ability to download the data presented on the ‘Family interaction’ and ‘Structure’ tabs as a tab delimited file. These files can easily be opened with most spreadsheet applications and are well suited to machine processing.