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For some structural study I am looking for cyclodextrin strucutures (in 3D format such as pdb, mol2, etc) complexed with small molecule ligands, such as cholesterol and even smaller. Right now I could only find on the PDB database some proteins complexed with cyclodextrin, but no structure of cyclodextrin with small ligands, could you help me?

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I looked for relevant publications at Web of Science using 'structur* AND cyclodextrin' in the Title field. For the period 2011-2012 there were 56 hits including:

Racz et al (2012) Structure of the inclusion complex of beta-cyclodextrin with lipoic acid from laboratory powder diffraction data. Acta Crystallographica Section B 68: 164-170

Ali et al (2012) Structure determination of fexofenadine-a-cyclodextrin complex by quantitative 2D ROESY analysis and molecular mechanics studies. Magnetic Resonance in Chemistry 50:299-304

Lula et al (2012) Interaction between bradykinin potentiating nonapeptide (BPP9a) and beta-cyclodextrin: A structural and thermodynamic study. Materials Science & Engineering C 32: 244-253

I looked at some of the papers but I didn't find any specific case where a structure has been deposited in a database. There were, however, several mentions of the Cambridge Crystallographic Data Centre as a source of small molecule structures.

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this is great! I will check whether the structures have been deposited somwhere –  flow Dec 4 '12 at 16:58
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