Sentence examples for binding pocket while the from inspiring English sources

Finally, comparison of the orientation of the hydrophobic binding site residues revealed that the side chain of V637 in Stat3 is pointed into the hydrophobic binding pocket while the corresponding residue V631 in Stat1 is pointed away from the pocket.

The cap moiety occupies the GTP binding pocket while the remaining of the RNA chain makes minimal interactions with the protein and appears stabilized by intra-molecular interactions as described in the next section.

Also, overlay of the Stat3 and Stat1 SH2 domain peptide backbone structures (Figure 3H) did not reveal superimposition throughout this region, particularly within LoopβC βD (K626DISGSTQIQS636), and the side chain of V637 in Stat3, which is pointed into the hydrophobic binding pocket, while the corresponding residue V631 in Stat1 is pointed away from the pocket.

In this particular case, the fatty acid is bound to the receptor so that the carboxylate and the electron-withdrawing groups (either nitro- or keto-) interact with polar residues in the binding pocket while the aliphatic chain is stabilized through hydrophobic interactions [ 26– 28].

Selectivity for uracil is mediated by several structural features: purine bases are sterically excluded from the active site by the overall narrow geometry of the binding pocket, while the entry of thymine and other 5-methylated pyrimidines is blocked by a side chain of a conserved tyrosine residue.

One subunit contains both the substrate and AMP binding pockets while the other subunit covers the opening to the binding sites (Fig. 7A).

To allow significant perturbations within the binding pocket while preventing the peptide and protein to separate during energy minimization, the refinement step begins with decreased and increased weights for the repulsive and attractive van der Waals term in the energy function, respectively.

Residues on one side of the peptide, including Tyr3, Tyr6, Trp10, and the disulfide bond, engage in hydrophobic interactions with the ephrin-binding pocket while the opposite side of the bound peptide remains mostly exposed to the solvent.

The C-terminal of chain D is also displaced towards the propanol binding pocket, while on chain B the movement is in the opposite direction.

Thus, computer modeling indicated that activity of a compound against Stat3 derives from its ability to interact with the binding sites for the pY and the +3 residues within the binding pocket, while selectivity for Stat3 vs. Stat1 derives from the ability of a compound to interact with the hydrophobic binding site, which served as a selectivity filter.

Overall, the computational studies mirror the findings from NMR experiments: the heteroaryl nitrogen directs oxoanions toward the binding pocket while diverting halides to settle with the weak C H hydrogen bond.