Chemical Structure Search

 

Using ChemAxon's Marvin for JavaScript editor, you can draw a chemical structure and search for exact, similar or substructures-of small molecules in the PDB.

The chemical structure can be drawn in the form of a chemical diagram and will be checked against all small molecules in the wwPDB chemical component dictionary that can be found in PDB structures as free ligands (not part of a polymeric chain of a protein or nucleic acid) or as non-standard residues (modified amino acids or nucleotides).

In the results page you will get all the PDB structures with such chemical components and in the "Ligand Hits" tab, the small molecules that matched.

In the "Chemical Structure Search" page you can load the chemical diagram of an existing chemical component and use it as a starting point, while whenever you come back to the page it will automatically load the last chemical diagram that you used.

The chemical search method is using the SMILES™ notations, so if you are familiar with them you may also use them directly as input for the Marvin for JavaScript editor.

SMILES™ (Simplified Molecular Input Line Entry Specification) is a linear notation for describing chemical structures.

You may consult the Marvin for JavaScript User's Guide in order to use the full capabilities of the Marvin for JavaScript drawing application by ChemAxon Ltd.

Elements of the Chemical Structure search page

  • Marvin for JavaScript editor: You may draw a molecule in the editor using the various provided options
  • Load SMILES textbox and button: Type a SMILES expression in the text area and click to load it in the editor ( Example: Clc1ccccc1 )
  • Load Chemical ID textbox and button: Type the three letter code of a PDB chemical component and click to load it in the editor ( Example: BMA )


Tutorial

 

Draw a chemical diagram in the MarvinSketch applet

Draw a chemical diagram
For example you want to search for small molecules in the PDB that contain a chlorobenzene fragment
  • Select the benzene group and add it in
  • Add an extra single bond to one of the atoms of the ring
  • Change the element of the atom on the other side of the ring to chlorine
  • Select the "Substructure" search option and click search
  • View the "Ligand Hits" tab in the results. All ligands have the chlorobenzene fragment


Watch the screencast

Draw a chemical diagram screencast



Use the "Any element" wildcard option

Use the Any Element type
Now you will replace chlorine in the input diagram with "Any Element"
  • Click on the Chemical Structure search page. You will have the chlorobenzene readily available since it was the last chemical structure you searched for
  • Click on the "Element" icon
  • Select the advanced tab and choose the A (Any) element type
  • Close the dialog and click on the Chlorine. It will now become an A.
  • Select the "Substructure" search option and click search
  • View the "Ligand Hits" tab in the results.


Use the "Not in list" wildcard option

Use the Not in list type
In this example you will replace the A (any) element type with "Any element except C,N and O"
  • Click on the Chemical Structure search page.
  • Click on the "Element" icon
  • Select the "Periodic Table" tab
  • Click on the "NOT list" button and then click on C,N and O
  • Close the dialog and click on the A (any) atom


Use the "Any bond order" wildcard option

Use the Any bond Order
Now you will change the ring type from aromatic to any kind of ring
  • Click on the "selection rectangle" icon
  • Click and drag a rectangle around the ring. All atoms become selected
  • Click on the arrow next to the single bond icon and choose "Any"
  • Select the "Substructure" search option and click search
  • View the "Ligand Hits" tab in the results.


Watch the screencast

Use SMARTS features screencast



Load the diagram of a PDB chemical component

Load a PDB ligand in the editor
You may load an existing PDB small molecule in the editor, modify it and use it for a search. In this example you will use Beta-D-Manose (BMA)
  • Type the 3 letter code e.g. BMA
  • Click on 'Load Chemical ID button'
  • Click on the arrow next to the single bond icon and choose the "Single Up" stereo configuration
  • Click on one of the bonds of the sugar ring
  • Select the "Exact" search option and click search
  • View the "Ligand Hits" tab in the results. Notice that you found all entries containing Alpha-D-Manose (MAN)


Watch the screencast

Load a PDB chemical component screencast



Other features


  • Select the Edit->Import Name menu of the applet and type in: lipitor. The MarvinSketch applet can draw diagrams from chemical names systematic or common
  • Select the File->Open menu of the applet and load your own molfile in the editor


Watch the screencast

Advanced MarvinSketch features screencast