Patent ID: 7662581

Claim:
A method for identifying an Eg5 binding ligand, the method comprising: (a) generating a three dimensional structure of an Eg5 protein using the atomic coordinates as set forth in Table 4 or Table 10 for all of the amino acids listed in Table 3 with a Root Mean Square Deviation (RMSD) for all heavy atoms being less than 2.5 Å, wherein said Eg5 is a kinesin-like motor protein that is localized to a mitotic spindle characterized by a motor domain having about 350 amino acid residues; (b) identifying a pharmacophore of a compound capable of binding with the said three dimensional structure of said Eg5 protein wherein said pharmacophore is: wherein B is benzyl, A is 3-aminopropyl, and Q is a group having a molecular moiety and wherein said pharmacophore binds at B and Q groups to the three dimensional structure of said Eg5 protein; (c) designing an Eg5 binding ligand with the based on said pharmacophore; (d) synthesizing said ligand; and (e) contacting said ligand with said Eg5 protein to determine an ability of said ligand to modify Eg5 activity thereby identifying said Eg5 binding ligand.