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Binding of single or multiple metabolites to the binding pockets of the transcription factors may change their protein conformations, which in turn modulate the transcription factor binding to the regulatory regions of the DNA.
The binding pockets of the enzyme for l-arabinitol, NAD+, and Zn2+ have been explicitly defined.
According to the binding modes, curcumin could efficiently fit within the respective binding pockets of the eight enzymes.
Rational residue substitutions were guided by the structure and properties of the binding pockets of the enzyme's active site.
Virtual screening of databases was carried out to identify novel compounds on the basis of difference between the binding pockets of the two proteins.
Molecular docking studies indicated that the synthesized compounds could occupy both p-amino benzoic acid (PABA) and pterin binding pockets of the dihydropteroate synthase (DHPS), suggesting that the target compounds could act by the inhibition of microbial DHPS enzyme.
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The crystal structure reveals that the compound extends out of the narrow binding pocket of the TNKS2 (Fig. 4).
This nest sits adjacent to the cGMP binding pocket of the B-site.
The molecular docking analysis demonstrated that these congeners occupy the colchicine binding pocket of the tubulin.
The compounds were initially docked into the binding pocket of the homology model of 5-HT3 receptor using GOLD program.
"If we look at the part of the gene that encodes the binding pocket of the receptor — it's very similar," Edsinger said.
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