Are you multitenant ? If so, probably best to get to the point where we're heading anyway with Apex, that is, an installation into the pluggable database and *not* in the container.
See
http://joelkallman.blogspot.com.au/2016/03/an-important-change-coming-for-oracle.html Assuming you've not used Apex 4 in your 12c instance, I'd be inclined to deinstall it first, and then install Apex 5. There's an "apxremov" script in the installation directory, but double check the installation guide for each release.
Hope this helps.