View source for B. Comparing the interactions of different ligands with the same target

'''i)'''	Return to the ligand entry of '''1f0r'''. Select '''Similar Binding Site Search''' at the top of the page. In the resulting '''Binding Site Analysis page''', type 100% in the '''Minimum Sequence Identity''' box and 2.5 in the '''Lowest Resolution''' box. Click on '''Submit'''.

'''ii)'''	A total of 45 structures are found. If this was a drug discovery project we would select all of the structures in order to include as much diversity of the ligands as possible. For a clearer picture we will limit our selection to 5 structures. Click on '''Invert Selection''' in order to de-select all entries. Select the following entries: '''1nfy''', '''1nfx''', '''1nfw''', '''1ksn''', and '''1xka''' by ticking the boxes next to the structure names. A total of 5 entries. Type 8.0 in the Radius of sphere around Ligand box, and click Submit.

'''iii)'''	In the Superposition Analysis page that comes up there is a lot of information about differences between the reference structure and the other structures that is presented in table form. Click on '''Show in ReliView''' to study all of the structures.

'''iv)'''	Use the Protein Explorer to switch off the displaying of entries '''1nfy''', '''1nfx''', and '''1nfw''' this is done by un-ticking the boxes next to the structure names in protein explorer. Compare the interactions of the remaining ligands in '''1f0r''', '''1xka''' and '''1ksn'''. Find waters 12 and 170 in the reference structure ('''1f0r''') through the protein explorer (expand the ‘water-tree’) – are the waters retained in '''1ksn''' and '''1xka'''? What is the difference between the interaction of '''1f0r''' and '''1ksn''' in the S1 pocket?

[[Image:relibase_workshop4.jpg]]

'''v)'''	Invert your selection – de-select '''1xka''' and '''1ksn''' (keep the reference structure 1f0r displayed) and select '''1nfy''', '''1nfx''', and '''1nfw'''. How has the ligand-protein interaction changed? Check waters '''12''' and '''170''', are they retained in all of the structures? Study the interaction of the ligands in '''1nfy''', how do they differ from the reference structure '''1f0r'''?

'''vi)'''	The ligands in '''1nfy''', '''1nfx''' and '''1nfw''' are known as reverse binders. The reversal of the binding pose can be explained by a number of ‘new’ interactions. The two waters in the S1 pocket are now completely displaced, which is likely to be thermodynamically favourable. The S4 interaction of the (cationic) basic moiety is explained by cation-pi interactions. There is also an unusual interaction between the chloride and the phenyl ring of Tyr228. Create a centroid of Tyr228 in 1nfy by selecting the menu Calculate -> Centroid -> New centroid. Pick the atoms in the phenyl ring of Tyr228 then click OK. A red dot should appear in the center of the phenyl ring. Measure the distance between the chloride of the ligand and the centroid of Tyr228 – this done by selecting '''Measure Distances''' in the '''Picking Mode''' box at the top of the ReliView window and picking the red dot in the center of the phenyl ring (the previously created centroid) and the chloride atom on the ligand.

'''This ends Part2B''' - [[ C._Validating_an_unusual_interaction_using_substructure_searching_in_Relibase|Part2C]] - [[Building_Solid_Foundations_for_a_Structure_Based_Design_Campaign_%E2%80%93_Workshop_handout_Erice_2008|Back to Start]]


[[Category:Software]]