Organs are not working with extra pedal ultimately (5)
I believe the answer is:
offal
'organs' is the definition.
(offal is a kind of organs)
'not working with extra pedal ultimately' is the wordplay.
'not working' becomes 'off' (switched off).
'with' means one lot of letters go next to another.
'ultimately' indicates one should take the final letters.
The final letters of 'extra pedal' are 'al'.
'off'+'al'='OFFAL'
'are' is the link.
(Other definitions for offal that I've seen before include "Carrion" , "Liver, kidney, etc, as food" , "Liver, kidneys etc - rubbish" , "Meaty waste" , "Edible heart, liver and tongue, for instance" .)