PDA

View Full Version : Spacer group


pugdom
Apr 1, 2009, 07:12 AM
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 ?

templelane
Apr 1, 2009, 10:19 AM
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.

pugdom
Apr 1, 2009, 02:05 PM
A little bit... But why is the -ch2- group often used... Is there any particular reason ? That this particular group is favourable ?

Thanks

templelane
Apr 3, 2009, 01:30 PM
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.