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Published online before print April 23, 2008, 10.1110/ps.033910.107
Protein Science (2008), 17:1129-1137. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 The Protein Society
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Cl–{pi} interactions in protein–ligand complexes

Yumi N. Imai1,2, Yoshihisa Inoue3, Isao Nakanishi1, and Kazuo Kitaura1

1 Department of Theoretical Drug Design, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
2 Discovery Research Center, Pharmaceutical Research Division, Takeda Pharmaceutical Company, Ltd., Osaka 532-8686, Japan
3 Product Strategy and Planning Department, Takeda Pharmaceutical Company, Ltd., Doshomachi 4-1-1,Osaka, 541-0045, Japan

(RECEIVED December 6, 2007; FINAL REVISION April 17, 2008; ACCEPTED April 18, 2008)

During systematic analysis of nonbonded contacts in protein–ligand complexes derived from crystal structures in the Protein Data Bank, Cl–{pi} interactions have been found, not only in the well-documented serine proteases but also, to a lesser extent, in other proteins. From geometric analysis of such Cl–{pi} interactions in the crystal structures, two distinct geometries were found: the "edge-on" approach of a Cl atom to a ring atom or C–C bond and the "face-on" approach toward the ring centroid with an average interatomic distance of 3.6 Å. High-level ab initio calculations using benzene–chlorohydrocarbon model systems elucidated that the calculated Cl–{pi} interaction energy is –2.01 kcal/mol, and the dispersion force is the major source of attraction. We also discussed the geometric flexibility in Cl–{pi} interactions and a relationship between the intensity of the {pi} density in an aromatic ring and the interaction position of the Cl atom.

Keywords: protein–ligand interaction; Protein Data Bank (PDB); Cl–{pi}; interaction; ab initio calculation; dispersion interaction


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