The proposed 239m tower, which would rank as the tallest building in Docklands and only be overshadowed by the Shard, will be mainly residential with 864 flats and 84 serviced apartments.
It will be located on the site of the City Pride pub in Westferry Road, which will be demolished to make way for the new tower.
Chalgrove Properties also lodged a separate planning application with Tower Hamlets council for the Island Point Site on Westferry Road, where it hopes to build 170 flats in a series of lower rise buildings from three to six storeys with rooftop pavilions.
Both sites were owned by Irish developer Glenkerrin, which received permission for a 62-storey tower in 2009.
But the group fell into administration in 2011 allowing Chalgrove to buy the sites from administrator Grant Thornton.