Structure binding sites

TAR, a 59-residue stem-loop structure binding site for Tat... 

Figure 6.6. Relibase home page. Relibase provides resources for searching/retrieving structures, binding sites of receptor proteins, and chemical diagram of ligands. All nonprotein moieties (except water) in the PDB complexes are considered as ligands.

The design of selective and potent inhibitors of PPIases is of interest and numerous molecules have been designed or selected from chemical libraries with a view to curing these major diseases. The study of Pinl, which is clearly distinct from other members of the PPIase family on the basis of structure, binding site, catalytic mechanism, and biological implications, has opened up new perspectives in the biological chemistry of PPIases. The recent discoveries of the secondary amide peptide bond cis-trans isomerase (APIase) DnaK [209] and of a novel class of FK506 and cyclosporine-sensitive PPIase [210] are also major advances in this field. 

The structured binding sites of metalloclefts mean that they are often highly selective hosts. An example is the salophen-uranyl-based metallocleft 3, which complexes neutral molecules, provided that the two phenyl groups of the host are parallel to one another. The salophen-uranyl unit may be employed as a catalyst for Michael additions, and the high steric requirements of the metallocleft of 3 result in it acting as a highly selective supramolecular catalyst. Metalloclefts of Type 4 selectively bind SO2 molecules and may be incorporated into dendritic materials that show catalytic activity. ... 

Since he was working in an institute for organic chemistry and biochemistry, he was familiar with the work of the Israeli s Katchalski-Katzir and Patchornik, who used polymers as supports for enzyme immobilization and for performing reactions on functional polymers. It was also the time when the mechanism of chymotrypsin was elucidated. This led Wullf to contemplate the possibility of producing synthetic polymers with catalytic sites that worked in the same way as enzyme active sites. There was already some literature on using synthetic polymers as catalytic models of enzymes but these did not have specific structural binding sites as enzymes did. Clearly a new approach would be required to generate such sites with specific predetermined structure. 

Desjarlais R L, R P Sheridan, G L Seibel, J S Dixon, ID Kuntz and R Venkataraghavan 1988. Using Shap Complementarity as an Initial Screen in Designing Ligands for a Receptor Binding Site of Know Three-Dimensional Structure. Journal of Medicinal Chemistry 31 722-729. 

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