With the percentages you quote – put the money in an ISA at 3%, and you will be just under £100 p.a. better off than paying off some of the mortgage.
Even if your mortgage were 5% and the ISA 3%, I would still advise you to invest the money in the ISA and not pay off the mortgage. My reason for this is that it is wise to have reserve capital for emergencies (unemployment, unexpected household repair, car repairs etc).
If you were to pay off the mortgage and find you suddenly needed to borrow £5,000 – you would be hard pressed to find someone willing to lend you the money (un-secured) at less than 10% interest.
I would also recommend you contemplate how you will enjoy this £5,000 – that is what it is for.