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Published online before print April 23, 2008
Protein Science, DOI: 10.1110/ps.033910.107
 Copyright © 2008 The Protein Society
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Cl-{pi} interactions in protein-ligand Complexes.

Yumi N Imai1,4, Yoshihisa Inoue2, Isao Nakanishi3, and Kazuo Kitaura3

1 Takeda Pharmaceutical Company Limited;
2 Takeda Pharmaceutical Company, Limited;
3 Graduate School of Pharmaceutical Sciences, Kyoto University

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

During systematic analysis of nonbonded contacts in protein-ligand complexes derived from crystal structures in the Protein Data Bank, C1-{pi} interactions have found, not only in the well documented serine proteases but also, to a lesser extent, in other proteins. From geometry analysis for such C1-{pi} interactions in the crystal structures, two distinct geometries were found: "edge-on" approach of a Cl atom to a ring atom or C-C bond and "face-on" approach towards 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 geometry 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: Structure; ab initio calculation; protein-ligand interaction

4 E-mail: imai_yumi{at}takeda.co.jp


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