Other than scanning for it (which I highly recommend you don't do as you said that your structure is huge so it would take a long time and might crash the game), I would say it isn't possible. If you are the one adding the structures (ie other custom structures) you could store their coords and sizes into a list and check against that.
I would suggest taking a look at how the game handles strongholds.
Thanks for advice, but i did it previously. I don't understand some parts of it for now, but it looks like it doesn't check intersection, and I think it is not matter for it cause it have rather small size.
Can't say exactly is that true or not, but i'll clear up it later(and post it if finde somthing helpfull)
Anyway for first time i made list with structures coordinates for checking another existing structures.