Patent ID: 8003572

Claim:
A method of determining a selective interaction between an ubiquitin conjugating enzyme (Ubc) and an organic compound comprising the steps of: a) inputting 3-D co-ordinates of a fragment of the ubiquitin conjugating enzyme into an electronic storage medium, wherein said fragment is less than the complete 3-D co-ordinates of said ubiquitin conjugating enzyme, using refined homology modeling or the crystal structure of said ubiquitin conjugating enzyme; b) determining a catalytic active site capable of forming a thioester adduct with ubiquitin in said fragment of the ubiquitin conjugating enzyme; wherein said catalytic active site encompasses a region on said ubiquitin conjugating enzyme within a 20 Angstrom radius of the catalytic cysteine of said ubiquitin conjugating enzyme; c) simulating a binding interaction between said active site in the fragment of the ubiquitin conjugating enzyme and a modified library of organic compounds, wherein said modified library of organic compounds is a library of organic compounds which have been altered by protonation to include hydrogens; d) identifying compounds in said library of organic compounds that interact with said active site in said fragment of step (c) of the ubiquitin conjugating enzyme, and e) then manually selecting the highest scored compounds and eliminating those compounds which excessively protrude out of the binding site, as visualized by the computer 3-D structure of the Ubc with the docked organic compound, one compound at a time.