Structure Gallery

Our research often deals with molecular structures, and below you can find a list of examples we uploaded to this gallery. In each case, there is a reference publication (when available) and a brief explanation. The link to each structure will get you to a separate page that automatically opens the J(S)mol viewer, which should work on modern browsers. If you experience issues with the viewer, please try a different OS or browser.

Comparison of crystal and docked binding poses of ligand 30 (BAZ2B)

Binding mode of compound 30 (see reference publication below) in BAZ2B. The crystal (PDB code 5ORB) and docking binding poses are essentially identical with the main difference found in the methoxybenzene tail, which contacts an adjacent protein chain of a crystal symmetric unit and is affected by significant anisotropy (bottom part). Six bromodomain-family conserved water molecules are visible with added hydrogens. In addition, a part of an adjacent chain in a crystal symmetric unit is present as chain Z (cf hereafter).

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Abeta fibril elongation: Docked states D1-D3

These are the three docked states, D1-D3, we used to understand the locking pathways and dynamics of Aβ1-42 fibrils based on the model from Riek's lab (2BEG, solution NMR). The three states were aligned according to the chains C, D, and E, which retained the template's structure throughout the simulations. They are contained as separate models (as in an NMR structure), and you can use the Jmol interface to display them separately or all at once.

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Comparison of crystal and docked binding poses of a 3-amino-2-methylpyridine ligand of BAZ2B

Superimposition of the crystal pose (PDB code 5L96) of compound 1 (of the reference publication below) and its docked pose. Six bromodomain family-conserved water molecules are visible (with added hydrogens).
The docked pose of compound 1 overlaps with the crystal structure even though the docking was carried out with the enantiomer not observed in the crystal.

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Chemical probe for DNA-repair enzyme MTH1

The fragment was identified by merging two hits obtained from docking a library of aspartic protease inhibitors in the binding site of MTH1. Further hit optimization was guided by molecular dynamics simulations. Ligand design was then validated by crystallography (PDB code 6EQ7).
The aspartate residues 119 and 120 establish hydrogen bonds, in a similar fashion as the analogous residues in the aspartic protease BACE1. The phenylalanine 27 is involved in an edge-to-face (T-shaped) interaction with the 3-fluoro-pyridine of the fragment.

To visualize the ligand (in magenta) and the residues Phe27, Asp119 and Asp120, copy the following script into the corresponding box and hit "Apply":

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