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Analysis of mapping between pharmacophores of different binding sites and each compound demonstrated that these benzamide derivatives bind at the dimer interface of the rabbit muscle enzyme, and possible docking modes of compound 4m were explored by molecular docking simulation.
C H HSQC experiments suggest compounds 2 and 3 also bind at the dimer interface of HSV-2 Pr.
To determine whether our new inhibitors 2 and 3 bind at the dimer interface, we first performed selective [C-δ1- methyl]isoleucine labeling for analysis by C H HSQC spectroscopy.
Across representative proteases from all three subfamilies, selective C/H [δ1- methyl]Ile data indicate compounds 2 and 3 bind at the dimer interface in the core of the Pr monomer >10 Å from the active site.
Allosteric small molecules that bind at the dimer interface of several caspases, including caspase-3, induce large conformational changes in active site loops, resulting in a zymogen-like conformation that is inactive (see Figure 1).
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We also present a crystal structure of the IN core domain in complex with sucrose which is bound at the dimer interface in a region that has previously been reported to bind integrase inhibitors.
Although the electron density for 11 clearly shows that the proximal half of the molecule binds at the dimer interface, the very weak electron density for the distal half precluded a reliable interpretation in terms of a molecular model.
This crystal structure confirmed that the small molecule bound at the dimer interface in a transient hydrophobic pocket formed by rotation of the tryptophan indole side chain causing the structural changes diagramed in Figure 20.
Colchicine is known to bind at the intra-dimer cleft in between the α- and β-subunits of tubulin heterodimers and induce a conformational change in tubulin from the straight GTP-bound conformation to one that mimics the bent GDP-bound conformation.
In this model, they bind a pocket at the dimer interface, >10 Å from the active site.
The FAD of each protomer is bound at the AB dimer interface, with both protomers contributing to the binding of FAD.
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