It can be a source of pain when the sun is up (5)
I believe the answer is:
sinus
'it can be a source of pain when' is the definition.
The definition suggests a singular noun which matches the answer.
'sun is up' is the wordplay.
'up' says the letters should be written backwards (in down clue: letters go upwards).
'sun'+'is'='sunis'
'sunis' back-to-front is 'SINUS'.
'the' acts as a link.
Can you help me to learn more?
(Other definitions for sinus that I've seen before include "Air-filled cavity of the skull" , "Anatomical cavity" , "Bodily cavity" , "Airspace" , "Hollow space" .)