A Boston-based gourmet pizza parlor chain that has struggled with labor troubles, financial problems and ownership disputes has filed for bankruptcy protection.

Upper Crust, which defaulted on its loan to TD Bank in late September, said it owes at least $3.4 million, including more than $500,000 to a Brookline construction company, and $229,000 to former Massachusetts Attorney General Thomas Reilly, who represented the business after leaving office, according to a list of creditors filed last week with the U.S. Bankruptcy Court in Massachusetts.

The Chapter 11 filing, which seeks protection from creditors while Upper Crust reorganizes, comes several days after the company shuttered its Waltham location.

A lawyer for the chain told The Boston Globe that Upper Crust's remaining 16 locations will maintain normal operations during bankruptcy proceedings.