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Description
The “Description” tab provides the following information:
1. Ligand name and chemical identifiers
On the left-hand side, you will find various information:
- Molecular Name and Synonyms: The standard name of the ligand, along with commonly used alternative names.
- Molecular Formula: The elemental composition of the ligand.
- Chemical Descriptors: Includes standardised identifiers such as IUPAC InChI, InChIKey and SMILES. These descriptors enable users to uniquely identify ligands and facilitate cross-referencing with chemical databases.
2. Structural Representations
Ligand structures are available in both 2D and 3D formats, with multiple views to highlight different structural aspects: overall shape, individual atoms, Murcko scaffolds, and specific ligand fragments.
- 2D View
- Accessible via the ligand image gallery shown on the right-hand side.
- Users can view simplified 2D depictions of the ligand, useful for quick recognition of functional groups, overall connectivity, scaffold and fragments.
- 3D View
- Accessible using the “View 3D” button.
- Two sets of 3D coordinates are provided:
- Idealised coordinates: represent a chemically “ideal” or neutral conformation, adhering to standard bond lengths, bond angles, and stereochemistry. These are generated using Molecular Networks’ Corina, and if there are issues, OpenEye’s OMEGA.
- Model coordinates: represent the experimentally observed conformation of the ligand, taken from the first PDB structure in which it was bound.
A. The Murcko scaffold highlighted in the 2D ligand image gallery, accessible by scrolling through the available images using the arrows next to the ligand diagram.
B. The Murcko scaffold highlighted in 3D after clicking View 3D. The menu in the top-left corner of the viewer allows selection of the conformer and the substructure to highlight.
Exercise
1. Identify the scaffold of this ligand.
2. Explore the different fragments present in this ligand.
(Hint: Use the arrows next to the ligand image gallery to see various ligand representations)
3. Visualise the scaffold in ligand's model conformation
4. Visualise the fragment in ligand's idealised conformation
3. Viewing atoms and bonds
The “View Atoms” and “View Bonds” buttons display comprehensive tables listing all atoms and bonds in the ligand, taken from the idealised conformation.