Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes

J Chem Inf Model. 2007 Mar-Apr;47(2):668-75. doi: 10.1021/ci6003527. Epub 2007 Feb 1.


We have performed a comprehensive analysis of water molecules at the protein-ligand interfaces observed in 392 high-resolution crystal structures. There are a total of 1829 ligand-bound water molecules in these 392 complexes; 18% are surface water molecules, and 72% are interfacial water molecules. The number of ligand-bound water molecules in each complex structure ranges from 0 to 21 and has an average of 4.6. Of these interfacial water molecules, 76% are considered to be bridging water molecules, characterized by having polar interactions with both ligand and protein atoms. Among a number of factors that may influence the number of ligand-bound water molecules, the polar van der Waals (vdw) surface area of ligands has the highest Pearson linear correlation coefficient of 0.63. Our regression analysis predicted that one more ligand-bound water molecule is expected for every additional 24 A2 in the polar vdw surface area of the ligand. In contrast to the observation that the resolution is the primary factor influencing the number of water molecules in crystallographic models of proteins, we found that there is only a weak relationship between the number of ligand-bound water molecules and the resolution of the crystal structures. An analysis of the isotropic B factors of buried ligand-bound water molecules suggested that, when water molecules have fewer than two polar interactions with the protein-ligand complex, they are more mobile than protein atoms in the crystal structures; when they have more than three polar interactions, they are significantly less mobile than protein atoms.

MeSH terms

  • Binding Sites
  • Computational Biology
  • Crystallography, X-Ray
  • Ligands
  • Models, Molecular
  • Protein Binding
  • Protein Structure, Tertiary
  • Proteins / chemistry*
  • Water / analysis*
  • Water / chemistry*


  • Ligands
  • Proteins
  • Water