A word of thanks, having got men aboard vessel (5)
I believe the answer is:
aorta
'vessel' is the definition.
(blood vessel)
'a word of thanks having got men aboard' is the wordplay.
'word of thanks' becomes 'ta'.
'having got' says to put letters next to each other.
'men' becomes 'or' (military abbreviation for Other Ranks).
'aboard' means one lot of letters goes inside another.
'a'+'ta'='ata'
'ata' enclosing 'or' is 'AORTA'.
(Other definitions for aorta that I've seen before include "main arterial route" , "vital transporter" , "Large artery of the heart" , "claret supplier" , "Principal artery" .)