BERLIN, June 12 (Reuters) - Novartis said on Monday that it has entered in an agreement to acquire U.S.-based Chinook Therapeutics for $3.2 billion upfront, with the deal expected to close in the second half.

The transaction is in the form of a merger of a newly formed Novartis subsidiary and Chinook, which has two high-value, late-stage medicines in development for rare, severe chronic kidney diseases, the pharmaceutical company added in a statement.

Under the agreed deal, holders of Chinook common stock would receive $3.2 billion in cash upon closing, plus a contingent value right with a value of up to $300 million, payable in cash upon the achievement of certain regulatory milestones, it said.

(Writing by Miranda Murray; Editing by Kim Coghill)