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Using Ketcher to Draw Chemical Structures

CDD Vault provides Ketcher as a tool for entering chemical structures into your vault.  Ketcher requires no installation and it helps you import, draw, edit, convert and save chemical structures in all of the popular chemical formats. 

The primary uses for Ketcher in CDD Vault are registering molecules in the registration system, inserting structures and reactions into the ELN, and searching chemical structures over your CDD Vault Platform.  Having quick access to Ketcher also comes in handy if you just need to draw, open or save a compound or reaction during your workday.


Ketcher Structure Editor

Opening Ketcher
The Canvas
     Selecting Structures
     Transforming Structures

Drawing Chemical Structures
     Insert Structure Lookup Tool
     Drawing Rings, Atoms and Bonds
     Using Enhanced Stereochemistry
     Adding R-groups to your Structure

Drawing Query Structures
    Atom Lists:
    The Extended Table for Generic Atoms and Groups
    Special Query Features


Ketcher Structure Editor

Opening Ketcher

Launch Ketcher in CDD Vault by clicking on the 'Explore Data' tab and then the 'Launch the Structure Editor' button in the structure search area.  Chemical structure search is the most easily available Ketcher button (1) but you can also open the editor by clicking in the 'Molecules' tab and 'Create a new molecule' (2) or by clicking on the hexagonal benzene icon in the ELN search bar (3). 





The Canvas

On launching the structure editor you will see the Ketcher canvas ready to paint.  Click on the 'full screen' arrows in the upper right side of Ketcher to maximize the canvas. Your small window or full screen preference will be remembered as long as you are in this session on your browser.



Selecting Structures:

Select tool: Once there are structures on the canvas you can perform actions on any single bond or atom by clicking on that entity.  Select all or part of a structure using the rectangle select tool or the freehand 'lasso' (see above). Selecting the pentane ring will select the whole fragment you click on next and highlight it in green.

Select tool hotkeys: 
     ctrl-A  to select everything on the canvas.
     ctrl-click to select an entire fragment
     shift and then make more selections while maintaining your current selection.



Transforming Structures:

Move  the whole drawing by clicking the top left button, the hand, and then drag the whole structure around the canvas.  Move a selection by highlighting any part or all of a structure and then dragging it where you want it.  If the selected atoms are connected to ones that are not selected, Ketcher will lengthen bonds to accommodate the move.

Rotate:  The 'rotate' tool allows you to rotate or flip a selected fragment or if there is no fragment selected you can rotate or flip the whole canvas.

First use the select tool to highlight the structure or part of a structure you want to change.

To rotate, click on the rotate tool and then click on the highlighted atoms and rotate by dragging the mouse.



To flip the selection expand the rotate tool and select the vertical or horizontal flip options.  Note that a fragment bound to unselected atoms will not flip.  Also, flipped compounds maintain their stereochemistry they're flipped like a pancake, not a mirror image.


Rotate/Flip hotkeys:  
     Alt-R: selects the rotate tool
     Alt-V: flips the canvas or selection vertically
     Alt-H: flips the canvas or the selection horizontally.



Drawing Chemical Structures

CDD Chemistry and Ketcher provide a fully functional tool for drawing chemical structures and reactions for searching, registering and recording chemistry in all of your CDD Vault modules as well as on your local documents.


Insert Structure Lookup Tool

When you're working in the CDD Vault platform, there's no need to draw each structure from scratch.  Use the Insert Structure tool in the upper right corner of Ketcher to pull a chemical from the database.  As you type a common chemical name, IUPAC name, CAS number or registration number, CDD Vault will fill in a type-ahead list of search results.  Clicking on the result will draw that chemical structure on the canvas.



Drawing Rings, Atoms and Bonds

Drawing and editing of structures uses the toolbars all around the the Ketcher canvas.  We'll give you a basic guide here, look to the advanced structure-drawing articles for more in-depth coverage.

Drawing Rings:  The ring templates buttons are on the bottom edge of Ketcher.  To draw a simple ring, click on the desired ring from the line-up and then click on the canvas.  The ring will be inserted by itself if you click in open space (1).  Clicking on a bond will join your new ring to the existing one, aromatizing the structure if possible (2).  Clicking on an atom will draw your chosen ring with a single bond to the existing structure (3).  (See below)


The template "TP" button will open a menu of 14 different lists of substructure templates.  To add a molecule from one of these lists, select it and click on "Add to Canvas".  (See above)  

Also in the TP menu is a tab for Functional Groups.  Selecting and inserting these functional groups will add an abbreviated group like Ms, OEt or PO4.  Right-clicking on any of these nicknames will let you expand or contract the functional group in your drawing.



Drawing Atoms:  There are several ways to draw or specify atoms either by clicking on the atom buttons on the right side or using keystrokes.

  • Atom hotkeys: Hover over an existing atom and then click the hotkey for the atom you would like to insert in its place.  All of the atoms on the right edge of Ketcher have hotkeys.  Hotkeys are pretty intuitive, but you can hover over the atom in the list to see its hotkey as a tool tip e.g. the hotkey for Chlorine is 'shift-C'.   When hovered over an atom on the palette you can also replace atoms with query atoms (A, M, X, Q below) or delete hovered-over atom using the delete key.

  • Click on the atomic symbol or hit the atom hotkey of the desired atom in the atom menu or in the periodic table -PT- in the atom menu.
    Once the atom you want is 'armed' then draw it by clicking in empty space (1 below), click on an existing atom to change to the highlighted one (2) or click and drag from an existing atom (3).

    atombutton.jpg      PTable.jpg

  • With the select tool selected, double-click an atom to open its properties dialog.  Here, changing the atomic label will change the atom.  



Drawing Bonds

Use the bond tool to select what bond type you want to insert or change a bond to.  Hovering over any bond in the tool will give you a pop-up label for the bond if the symbols are not absolutely clear (below).

Draw a new bond by clicking on an atom and dragging away from it or change a bond type by clicking on it with a bond type selected in the bond tool.  Clicking on a single bond will upgrade it to a double bond, clicking again makes it a triple, one more click and you're back to single.

To bring up the bond properties box, with the select tool button highlighted, double-click on a bond.  There are several criteria you can set for the bond, see below.




Using Enhanced Stereochemistry

Using Ketcher as your drawing tool in CDD Vault you can represent stereochemistry using enhanced stereo notation.  Drawing a molecule using an up or down wedged bond will default to the absolute stereochemistry option in Ketcher. 

Note: if a structure is copied from another drawing, the enhanced stereochemistry flag may not be enabled.  If this is the case, the stereochemistry button will be disabled/grayed out and you won't see the 'ABS' flag near the structure. Deleting and redrawing the bond in Ketcher will resolve this trouble.

To represent a compound as either a mixture of multiple isomers (AND group) or as a pure, still unidentified isomer (OR group) then use the 'Stereochemistry' button at the top of the canvas.  Draw the structure in one one of it's absolute configurations and then click on the Stereochemistry button.  (See below)



This is a simple example with only one stereocenter.  Take a look at our knowledgebase article "Advanced Stereochemistry Registration: Atropisomers, Mixtures, Unknowns and Non-Tetrahedral Chirality" to learn about AND/OR configurations with multiple chiral centers.


Adding R-groups to your Structure

Use the R-group tool in the left-side toolbar to define a group of fragments and their attachment points.  The R-group tool has three different functions, all necessary for defining R-groups. Click on the lower right corner of the tool to expand the buttons to all three.

Note that in the structure search drawing tool in the explore data tab, only the label tool is available for queries.  Use atom lists or query atoms to search for multiple possibilities.  (See Structure-searching in CDD Vault for more.)


  1. The R-group label tool to identify where R-groups are tied to the base structure
  2. The Fragment tool for defining the fragments for each R-label and
  3. The Attachment Point tool to identify where the fragment is bound to the base structure

With the three tools there are three steps to defining R-groups. 

First, draw your base structure with a bond with any atom where your R-groups will go.  Now click on the R-group label tool and then on the atom you want to change to an R-group.  You'll be presented with a dialog where you pick the number of the R-group you want to assign to this atom. Select the label you want and click *Apply.  See below where two other R-group labels have already been created.


Next, draw your R-group fragments on the canvas.  In the example below there are two different groups of fragments, these were drawn in groups near each other but this is not necessary.  Once the fragments are drawn, assign each one to an R-group by opening the fragment tool , click on each fragment then assign it to an R-group.  If there are already fragments in an R-group with the number you assign the new one to, it will be added to the group in the square brackets.


The last step to creating an R-group is to define the attachment point(s) for each fragment.  To do this, open the attachment point tool (#3 in the R-group tool above) and then click on the atom that will be tied to the R-group label on the base molecule. 


Drawing Query Structures

Atom Lists:

To create a query structure with multiple atoms at one position you draw the structure with an atom list.  Inserting a list of atoms is the same as drawing a single atom from the periodic table except that you have picked multiple elements from the table.  Refer to the figure below to do the following: 

  1. Open the periodic table (PT) in the right bar of Ketcher 
  2. Select the 'List' radiobutton at the bottom of the table.
  3. Select all of the atoms you want to be in the list.
  4. Click 'Add' to arm your bond tool and close the PT
  5. Draw your list the same way you would draw an atom.



The Extended Table for Generic Atoms and Groups

Click on the extended table icon "ET" at the right edge of the canvas to see a list of generic Atoms, special atoms and groups.  Hovering over any atom or group in the table will bring up a tool tip explaining the generic entity that will be inserted into your structure. 

Generics can be very useful in drawing queries and looking for any Atom (A), Metal (M), Halide (X) or generic groups like Aryl (AR) or Alkenyl (AEL).  



Special Query Features

When drawing a structure for a query special query features can be applied by double-clicking on the atom and selecting the "Query Specific" menu.  Here you can set constraints for your query around counts of ring bonds, protons, substituents or check/uncheck the "Unsaturated" box.