Nonprotein-ligand complexes

Crown ethers are cyclic polyethers that form complexes with cations. Ligand specificity is highly dependent on the size of the crown ether cavity for example, 12-crown-4 binds Li but not K dicyclohexano-18-crown-6 bindsi K but not Li.  

Straatsma and McCammon estimated the free energy costs attributed to organization of the host in the binding conformation. They used the 

HIVl protease 3hvp 2.8 A P2—PI bond- fluoroethylene AMBER 

Protein PDB Resolution Mutation S Force Field NB-i SL NB SL AGf l AAGCfJfa AAGIfP, Ref. 

FK506BP Ifkg 2.0 A X-Phcnyl- X-pyridyl OPLS 9k 1.4x10 9A 1.4x10 0.6 0.1 0.9 -1.0 153 

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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.

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