I just created a new Pluggable database in my container, PDB2. I want to discover it in EM12c Rel 3.
Go to Setup -> Add Target -> Add Targets Manually
Choose "Add Targets Using Guided Process", for Targets type choose Oracle Database, Listener and ASM
Specify host, then click next
Input the pass and then Next
The confirmation window appears
Going to Targets -> Databases, you can find the pluggable database in the list.