As others have suggested, it looks very much like a substitution at the fluorine position. I might add that high resolution electrospray mass spec should be very useful in this case, because I suspect that this adduct will survive sample preparation, and it would provide strong and orthogonal experimental evidence that a chemical reaction had occurred at that position, specifically that fluorine had been lost during the reaction. To make your life easier, I’d definitely run an unreacted protein sample as a control (subjecting it to the full experimental procedure for creating the reaction.) The mass resolution of electrospray is amazing, but in many cases there are complications to the spectrum from associated ions. You definitely want the control spectrum for the unreacted protein to be from exactly the same solution conditions as your experimental sample.
> On Aug 23, 2017, at 10:01 AM, Cheng Zhang <chengzh1...@gmail.com> wrote: > > Hi everyone, > > We recently got a structure of a receptor bound to a ligand. The ligand has a > fluoro methyl benzene ring moiety, which is close to a Cys residue in the > receptor. The density for the ligand and the Cys seems to suggest a covalent > bond. However, I don't know if a covalent bond is chemically possible. Also, > I believe Cys is rarely involved in cation-pi interactions? Any suggestions > for placing the Cys and the fluoro methyl benzene ring? > > Thanks! > > Cheng > > <Screen Shot 2017-08-23 at 10.45.24-1.jpg> > > -- > --------------------- > Cheng Zhang
