You must have inadvertently upgraded your system pip (probably through
something like sudo pip install pip --upgrade)
pip 10.x adjusts where its internals are situated. The pip3 command
you're seeing is one provided by your package maintainer
(presumably debian based here?) and is not a file managed by pip.
You can read more about this on pip's issue tracker
You'll probably want to not upgrade your system pip and instead
use a virtualenv.
To recover the pip3 binary you'll need to sudo python3 -m pip
uninstall pip && sudo apt install python3-pip --reinstall.
If you want to continue in "unsupported territory" (upgrading a
system package outside of the system package manager), you can probably
get away with python3 -m pip ... instead of pip3.