[pugdom]

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]

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]

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

Thanks

[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.