Left church in ancient city, being sore (5)
I believe the answer is:
ulcer
'being sore' is the definition.
(I've seen this before)
'left church in ancient city' is the wordplay.
'left' becomes 'l' (common abbreviation).
'church' becomes 'CE' (abbreviation for Church of England).
'in' indicates putting letters inside.
'ancient city' becomes 'ur' (ancient Sumerian city state).
'l'+'ce'='lce'
'lce' put within 'ur' is 'ULCER'.
(Other definitions for ulcer that I've seen before include "Sore point" , "Cruel kind of body sore" , "Cruel kind of open sore" , "Continuing source of pain" , "Stomach or mouth sore" .)