binding cavity

The ligand binding cavities are located at the interface between the subunits.

A third method is the optimization of known ligands by evaluating proposed analogs within the binding cavity.

The E domain contains the ligand binding cavity as well as binding sites for coactivator and corepressor proteins.

In creating new MIPs, a compromise must be created between full removal of the original template and damaging of the substrate binding cavity.

The ligand binding cavity is within the interior of the LBD and just below three anti parallel alpha helical sandwich "filling".

Alternatively rotamer libraries of amino acid side chains that surround the binding cavity may be searched to generate alternate but energetically reasonable protein conformations.

A small conformational change permits the A or S side chains to extend into the binding cavity behind the triphosphate; S hydrogen bonds to the β-phosphate.

The bulky side chain, protruding from the binding cavity, displaces helix 12 from ligand-binding pocket to cover part of the coactivator binding pocket.

The binding cavity of the hypnotic agent propofol in the GABA receptor using a diazirine containing propofol analog.

The hydrophobic and shape complementarity between the peptide substrate P sidechain and the enzyme S binding cavity accounts for the substrate specificity of this enzyme.

Together, this pair forms a hydrophobic funnel that is suggested to serve as the insertion site for ubiquinone, in conjunction with the FMN binding cavity at the C-terminal.

At last, beta-2 Thr83 is rather remote from the ligands (8.5 A), but the side-chain of a lysine could come closer and influence lightly the electrostatic potential of the binding cavity.

The implicit solvation model breaks down when solvent molecules associate strongly with binding cavities in a protein, so that the protein and the solvent molecules form a continuous solid body.

Many ERβ-selective ligands have a largely planar arrangement as the binding cavity of ERβ is slightly narrower than that of ERα, however, this by itself leads to modest selectivity.

Although the size of the binding cavity in most N macrocycles, including porphyrins, can vary to only a small degree, a series of tropocoronand ligands (TC-m,n) having the same set of four aromatic nitrogen donor atoms but with a range of macrocycle sizes can be prepared.

Conformations of the ligand may be generated in the absence of the receptor and subsequently docked or conformations may be generated on-the-fly in the presence of the receptor binding cavity, or with full rotational flexibility of every dihedral angle using fragment based docking.