Ligand interaction map

Figure I. PNP Ligand Interaction Map. Ligand atoms or residues classified by their importance to ligand binding affinity.

Amadasi, A., Spyrakis, E., Cozzini, P., Abraham, D.)., Kellogg, G. E Mozzarelli, A. Mapping the energetics of water-protein and water-ligand interactions with the natural HINT force field predictive tools for characterizing the roles of water in biomolecules. J. Mol. Biol. 2006, 358, 289-309. 

Palzkill, T., Huang, W., and Weinstock, G. M. (1998). Mapping protein-ligand interactions using whole genome phage display libraries. Gene 221, 79-83. 

This kind of shift mapping has been used extensively in NMR studies of protein-ligand interactions. Shuker et al.1/2 used this method to advantage in a lead generation approach that effectively covalently links two... 

The analysis of the crystal structures of Cox2 with a selective ligand SC-558 (PDB [66] code 1CX2) and the nonselective Coxl/Cox2 inhibitor flurbiprofen (PDB code 3PGH) fully confirms the expectedly weak match between the pharmacophore models built by variable selection and the actual Cox2 interaction map. 

Naumann and Matter used a set of 26 X-ray structures of eukaryotic protein kinases, which were classified into subfamilies with similar protein-ligand interactions in the ATP binding site. As can be seen in Fig. 3.13, which shows the GPGA score plot, PC 1 separates CDK and MAP/receptor kinases on the left from the family of PKA kinases. The CDK family is represented by two distinct clusters in the target family landscape, formed by two different ATP binding site conformations. They correspond to the activated and inactivated kinase conformations... 

Figure31. Myoglobin-ligand interaction contour map in the xy plane at z = 3.2 A (seethe text). Distances are in A and contours in kcal the values shown correspond to 90, 45, 10,0 and —3 kcal/mol relative to the ligand at infinity. The highest contours are closest to the atoms whose projections onto the plane of the figure are denoted by circles.

Figure 32. Myoglobin-ligand interaction contour map in the xy plane aty = 0.5 A (see Fig. 31 legend).

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