Replacing a custom serial port connector with a Micro-USB 2 plug
The ominous Pin #5 is usually the ID Pin and does not travel through the cable. If I remember correctly, this pin is usually shorted to ground, indicating a device device or open, indicating a host device.
In other words: This pin decides if the device which is connected plays the host or device role.

If you use the other 4 pins, make sure that no user will really use a "normal" USB cable (and they will) as your device will most likely get 5V on the power pin (which is probably not what you want).  

PJCs solution is in my opinion a good one (but requires you to change the board)