Molecules, Targets and Isoforms
The short answer is no.  What matters is whether the sequence and folding (if you are talking about binding of A to proteins instead of DNA) of each isoform of your gene still results in the binding of A.  

I other words, A may bind to X. Y, an isoform of X may not have the same sequence that A likes to bind to. Or, in the case of proteins and A, Y may fold slightly differently, preventing accessibility of A to Y.