Run. The big thing is the quads, which aren't used to the different contractions required by running when your foot hits the floor. I think its referred to as eccentric contractions vs concentric contractions, but the more knowledgeable may correct me on that. If I return to running after a lengthy break, as I recently have, it takes me about seven to ten days to get past the muscle soreness in the quads and, to a lesser extent, the adductor muscles.

Just run at a very modest pace, preferring a high cadence, short-striding rhythm to look after your knees. Five weeks is plenty of time to prepare for a 5k if you are aerobically fit from cycling. Five minutes four times a week the first week, ten minutes the second, fifteen the third etc. by week five you'll be able to run 5k.