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Cited by 285

The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.

NH…O, OH…O, and CH…O hydrogen bonds in protein–ligand complexes: Strong and weak interactions in molecular recognition

Sarkhel, Sanjay, Desiraju, Gautam R.·2004·Proteins: Structure, Function, and Bioinformatics
DOI 10.1002/prot.10567
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Abstract

The characteristics of NH…O, OH…O, and CH…O hydrogen bonds are examined in a group of 28 high‐resolution crystal structures of protein–ligand complexes from the Protein Data Bank and compared with interactions found in small‐molecule crystal structures from the Cambridge Structural Database. It is found that both strong and weak hydrogen bonds are involved in ligand binding. Because of the prevalence of multifurcation, the restrictive geometrical criteria set up for hydrogen bonds in small‐molecule crystal structures may need to be relaxed in macromolecular structures. For example, there are definite deviations from linearity for the hydrogen bonds in protein–ligand complexes. The formation of CH…O hydrogen bonds is influenced by the activation of the C αH atoms and by the flexibility of the side‐chain atoms. In contrast to small‐molecule structures, anticooperative geometries are common in the macromolecular structures studied here, and there is a gradual lengthening as the extent of furcation increases. CH…O bonds formed by Gly, Phe, and Tyr residues are noteworthy. The numbers of hydrogen bond donors and acceptors agree with Lipinski's “rule of five” that predicts drug‐like properties. Hydrogen bonds formed by water are also seen to be relevant in ligand binding. Ligand CH…O w interactions are abundant when compared to NH…O w and OH…O w. This suggests that ligands prefer to use their stronger hydrogen bond capabilities for use with the protein residues, leaving the weaker interactions to bind with water. In summary, the interplay between strong and weak interactions in ligand binding possibly leads to a satisfactory enthalpy–entropy balance. The implications of these results to crystallographic refinement and molecular dynamics software are discussed. Proteins 2004. ©2003 Wiley‐Liss, Inc.

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Metadata

Authors
Sarkhel, S., & Desiraju, G. R.
Venue
Proteins: Structure, Function, and Bioinformatics
Publisher
Wiley
Published
2003-11-24
Volume
54
Issue
2
Pages
247-259
ISSN
  • 0887-3585 (ISSN-L)
  • 1097-0134
DOI
10.1002/prot.10567
OpenAlex
W2114589487
Cited by
285
References
30
FWCI
8.35
Type
journal article
Language
en
Open access
closed

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