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Crystallographic studies have revealed that vorinostat inhibits HDAC activity by binding in the active site of the enzyme (Finnin et al, 1999).
Furthermore, phenol alone and substituted phenols in general inhibit COX enzyme activity through binding in the active site, thereby obstructing enzyme kinetics (Hsuanyu and Dunford 1992), which signifies the inhibitory effect of the benzene group on the PG pathway.
Molecular modelling showed a strong correlation between activity and in silico binding in the active site of acetylcholinesterase.
Molecular modelling of both the TP inhibitors and XO-activated prodrugs rationalized their binding in the active site of the human TP crystal structure.
Overall, these data indicate that in addition to binding in the active site, RS2 can bind outside the active site enhancing substrate turnover.
The substantial changes we observed in kcat as a result of mutation of aspartic acid 139 in cPAH raised the possibility that destabilization of iron binding in the active site could be contributing to the reduction in enzymatic activity.
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The revealed difference in the modes of proton-binding in the active site might reflect independent transition to H+-ATPase in different lineages.
We first modeled the process of Mg2+-binding in the active site of FTase using information from experimental studies of FTase and similar systems in order to generate starting configurations for our studies.
It is, thus, very well possible that the enzyme has separated the oxygen binding and substrate binding positions in the active site of AlkB to prevent reactivity by the iron III)–superoxo species.
To study the binding mode in the active site of plasmodial ODC and to elucidate binding differences, PPT3 and PPT5 were modeled into the active site of PfODC (Figure 2).
In the opposite direction, ATP binding, situated in the active site cleft, also induces conformational changes and is coupled with distal substrate binding [50], [52] [54].
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