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In this way, binding pocket could be defined consistently across the same structural ensemble, varying in conformation but not in composition.
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In addition, many drug pairs with potential similar binding pockets could be discovered by the domain matching information.
By docking of the 2PET model substrate, the substrate-binding pocket could be identified as a large groove on the surface of Tcur1278 and Tcur0390 (Figure 4C-F).
When the scaffold is tethered at an appropriate position, a molecule that potentially interacts with the GABA-binding pocket could be a potent ligand, which opens a door for future PTL design.
To discover new KCNQ2 activators and to further verify the possible activator-binding pocket, we carried out a structure-based virtual screen targeting the identified pocket, guided by the notion that if the identified binding pocket is reasonable, novel activators recognizing the identified ztz240-binding pocket could be discovered.
Although the active site of phosphoglucomutase is highly conserved from parasite to human, initial calculations show that a ligand binding pocket could exist near the hinge region, which is unique to the parasite.
Residues 305 314 on the surface of the first subunit are not in a position to interact directly with the binding pocket, but could be involved in mediating interactions between the two subunits.
Of particular interest is the category of temperature-sensitive mutations in the Rb pocket domain (ΔAsn480, Arg661Trp, Cys712Arg) whose 'reversible fluctuations' in a threshold level of Rb pocket-binding activity could be responsible for their characteristic low penetrance (Otterson et al. 1999).
This is indicative of a change in binding mode or could be due to the phenyl ring in C12M02 occupying a new high affinity binding pocket.
This binding could be inhibited by heparin.
Replacement of water from the uncomplexed binding pocket is assumed to be entropically favorable.
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