そこは東京駅から5分くらいの所にありますって英語でなんて言うの？

Well, firstly; you obviously need to state what mode of transport you are using if you are talking about a travel time of 5 minutes.
There are 3 examples above using different formats, all of which are quite acceptable.

Five minutes is not a lot! So you can always make it seem like an easy task by using the word 'only'. Saying, "It is only five minutes from Tokyo Station." or, "It only takes five minutes from Tokyo Station." Allows the listener to image a short distance they know that only takes five minutes.

We will arrive at our destination in 5 minutes.

You can also refer to the arrival time. We will arrive in 5 minutes. We are 5 minutes away from our location.

The station will be coming up in 5 minutes.

There are numerous ways you can apply the vocabulary above using whatever time limit is necessary. (For example, our food will arrive in 30 minutes, The food is 30 minutes away)

If you leave from Tokyo station, it will take you 5 minutes to get to your destination
This informs the person that if their starting point is Tokyo station, then within 5 minutes they will reach their destination. A destination is the final place they intend to go to. This of course will dependent on their mode of transportation.

We giving time as related to distance you can use the words "only", "just", or "about" with give the time to or from a location as in: "about 3 minutes walk from..." or "just 5 minutes away by car".