The company had been seeking US protection from Russian government-ordered selloffs of its assets.
"We will now focus our efforts elsewhere to survive as a going concern and obtain compensation for assets that have been improperly expropriated from us," Yukos chief executive officer Steven Theede said in a statement.
Theede said a stay granted by the US courts helped preserve the value of Yukos' estate but Yukos spokesman Mike Lake said yesterday's court filing "in effect will end" Yukos' case.
Last week, US District Judge Nancy Atlas rejected a Yukos request for protection of the company's remaining assets while Yukos appealed a the dismissal of its Chapter 11 bankruptcy case filed in Houston in mid-December.
Yukos lost 60% of its oil production capacity with the Russian government-ordered December sale of a key subsidiary in Moscow.
The company argued that without legal protection it could disappear before an appeal ran its course if the Russian government ordered more asset sales to further pay a disputed $US27.5 billion ($A35 billion) back-tax levy.
Yukos filed for bankruptcy in Houston days before the December 19 auction of Yuganskneftegaz. The company's only US assets are two bank accounts. Its displaced finance chief operates out of his Houston home.
Clark blocked the sale, but the Russian government said its actions on Russian soil did not come under her jurisdiction. A shell company later acquired by state-owned oil company Rosneft bought the subsidiary.
Clark's ruling also meant Yukos had no US forum to sue alleged participants in the Yuganskneftegaz sale. This quashed the company's $US20 billion ($A25 billion) lawsuit against Gazpromneft, Gazprom, Rosneft and others.