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-   -   Spacer group (https://www.askmehelpdesk.com/showthread.php?t=336593)

  • Apr 1, 2009, 07:12 AM
    pugdom
    Spacer group
    What is meant by a spacer group ? And why are they used in relation between the molecule and its ability to bind to a receptor site ?
  • Apr 1, 2009, 10:19 AM
    templelane

    Sometimes to inprove the fit of a ligand to the docking site a spacer group is used. It is used to make the parts of the molecule which bind the active site sit in better positions. Sometimes a spacer group can also be used so that you can increase the ligand- receptor site interactions by extending into a part of the receptor site that could not be reached before.

    Does this make sense? If not I'll try and explain it better.
  • Apr 1, 2009, 02:05 PM
    pugdom

    A little bit... But why is the -ch2- group often used... Is there any particular reason ? That this particular group is favourable ?

    Thanks
  • Apr 3, 2009, 01:30 PM
    templelane

    It's kind of a middle of the road group, its not particularly hydrophobic like a ring group, it's pretty small, it's not polar and it's a pretty easy group to synthesis onto your compound.

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