[ Pharmacophore Draw 2D | Pharmacophore Draw 3D | Pharmacophore Search | Extract 3D pharmacophore | Color 2D ]

Pharmacophores can be drawn in 2D in the ICM Molecular Editor or in 3D in the Graphical Display. 2D pharmacophore sketches can be used to search chemical tables (spreadsheets) containing 2D or 3D coordinates. A 3D pharmacophore can be used to search chemical tables containing 3D coordinates only.

15.9.1 Pharmacophore Draw 2D

A 2D pharmacophore can be drawn using the ICM Molecular Editoror if you are going to use the drawing to search it is more efficient if you draw it in the Chemical Search window.

Use the distance bond button and the add pharmacophore group button to sketch the pharmacophore. The distance bond button represents the number of bonds between each pharmacophore point. You can edit the distance by right clicking on the bond and selecting edit. Other groups such as aromatic can be added using the standard molecular editor buttons.

NOTE: Do not mix the 2D and 3D pharmacophore environment. For example do not edit a 3D pharmacophore in the 2D editor.

15.9.2 Pharmacophore Draw 3D

The easiest way to begin drawing a 3D pharmacophore is to draw a chemical in the ICM Molecular Editor which contains the key pharmacophore groups you want and then convert to 3D and extract the pharmacophore groups.

To draw a 3D pharmacophore this:

• Once the ligand is converted to 3D, right click on the ligand in the ICM Workspace.
• Select the option Copy as Pharmacophore and choose the pharm centers option.
• The pharmacophore groups or centers will then be displayed in the graphical display and can be displayed and undisplayed in the ICM workspace.

To move a pharmacophore group:

• Use the drag atom button (picture of a hand. See below)
• Click on the pharmacophore group and then drag.

NOTE: Distances between groups can be monitored using the atom distance measurement tool. See Calculating the distance between two atoms.

To change a pharmacophore group:

• Right click on the pharmacophore group in the ICM Workspace or in the Graphical Display.
• Select Pharmacophore/Edit Point
• Choose the group from the drop-down list shown below.
• Enter the desired radius.

To make a new pharmacophore group:

The easiest way to make a new pharmacophore group is to clone a pre-exisiting one. To do this:

• Right click on the pharmacophore group in the ICM Workspace or in the Graphical Display.
• Select Pharmacophore/Clone Point
• You can then move the new group as described above.

To change the direction of a pharmacophore group:

• Right click on the pharmacophore group in the ICM Workspace or in the Graphical Display.
• Select Pharmacophore/Assign Direction
• You can then move the new group using the drag atom button described above.

To remove the direction of a pharmacophore group:

• Right click on the pharmacophore group in the ICM Workspace or in the Graphical Display.
• Select Pharmacophore/Remove Direction

15.9.3 Pharmacophore Search

To perform a pharmacophore search using a 2D pharmacophore:

• Draw the 2D pharmacophore as described earlier in the Chemical Search window.
• Read in a molecular table to search or search a table in MOLCART.
• Select the chemical search options as shown below.
• Once the search has completed a new table with the results will be displayed.

To perform a pharmacophore search using a 3D pharmacophore:

• Right click on the pharmacophore in the ICM Workspace
• Select Search Pharmacophore
• Use the drop-down button to select the table you wish to search. The table must contain 3D coordinates.

15.9.4 How to extract a 3D pharmacophore from a ligand.

15.9.5 How to color a 2D chemical sketch by pharmacophore feature.