Unfortunately no.
I am running a setup with a 2016 MacBook Pro, the Thunderbolt 3 to Thunderbolt 2 adapter and a 2013 iMac 27".
Edit: I was wrong. It is possible. You will have to press Cmd+F2 to active TDM with this configuration. My old iMac switches to TDM automatically. That's why I was confused, sorry!