Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile. [ http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE ]