The first RER B train from Notre-Dame St-Michel leaves at 05:39 and arrives at CDG at 06:14. Metro lines serving the Latin Quarter don't start running early enough for you to connect with that RER train, but you can easily walk to Notre-Dame St-Michel.
The above scenario gets you to CDG 90 minutes before your flight, which is adequate for a flight to another EU and Schengen zone country at that time of day. However, if you want to be at CDG a bit earlier, there are two early RER B trains that originate at Gare du Nord. The first one leaves there at 04:56 and arrives at CDG at 05:30. The second one leaves at 05:29 and arrives at 05:58. Take a taxi from your hotel to Gare du Nord.