Fig. 5: Analysis of hydrogen bonds and residue interactions in hHDAC8 upon PCI-34051 binding.
From: Binding mechanism and distant regulation of histone deacetylase 8 by PCI-34051
A Depiction of H-bonds within the structural domain encompassing L1, L2, L3, α1, α2, α4, and α5, as determined from the crystal structure (PDB ID: 3F07). Intrahelical hydrogen bonds have been omitted for clarity. The illustration does not include non-bonded main chain or side chain interactions. B Analysis of the perturbations in residue interactions upon PCI-34051 binding, as revealed by molecular dynamics (MD) simulations. Enhanced interactions between residues are indicated by red lines, whereas diminished interactions are denoted by blue dashes. The intensity of the color gradient corresponds directly to the magnitude of the interaction change. L3 is highlighted in blue on this structure.
