Crystallographic Packing Effects

Although the problems discussed above can impose some restrictions on the use of binding site comparisons in chemogenomics programs, the broad array of methods available still offers significant support for the majority of cases. Careful assessment of the target structure and the relevant structural data can certainly guide the choice of appropriate methods. For example, the application of methods 

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Figure4.7 Crystallographic packing effects in factor Xa binding sites, shown for PDB structures lfax and lxkb. lfax is shown with white carbon atoms, the superimposed lxkb structure (rms deviation of binding site Ca atoms 0.38 A) is omitted. The ligand of lfax is shown in green and the ligand of lxkb in magenta. Residues present in the crystal packing environment of lxkb are shown in yellow.

Figure 4.5 Example of how crystallographic packing effects can lead to ligand binding modes that are not biologically relevant. The yellow and green structure (PDB ID lqs4 the catalytic core domain of HIV integrase) shows atom coordinates generated by expanding symmetry-related molecules.

Bergner, A., Gunther, J., Hendlich, M., Klebe, G., and Verdonk, M. (2001) Use of relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects. Biopolymers (Nucleic Acid Science), 61, 99-110. 

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