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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



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

Use the "Any element" wildcard option

Use the Any Element type
Now you will replace chlorine in the input diagram with "Any Element"

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"

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

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)

Other features