The binding pocket consists of two loops (loop1 and loop2) in the amidase signature sequence and one helix (α10) in the non-amidase signature sequence.
In both cases, in silico studies were performed on full length CFTR structural model and binding pockets consisting of NBD1 and ICL4 residues.
The drug-binding pocket consists of 12 TM segments and has multiple and overlapping drug-binding sites.
The PFTase binding pocket consists mainly of large aromatic amino acids that act as the backstop for FPP.
The nucleotide corresponding to G130 is a U in the U4 snRNA Sm site, which is accommodated into the nucleotide binding pocket in SmD1 (Leung et al., 2011 ); (G ), U131 base is accommodated in a pocket consisting of SmD2 L3 residues His62 and Asn64, and L5 residue Arg102; (H ), G132 makes several interactions with the ribose phosphate backbone of neighbouring nucleotides.
We selected the amide hydrogen of E638 within the site that binds the +3 residue (Q, C or T) within the pY-peptide ligand [23] as the central point of the binding pocket, which consisted of a cube with dimensions 16.0×16.9×13.7 angstrom.
The interactions are mostly hydrophobic and van der Waals with the CA-CTD binding pocket, which consists of residues Phe168, Leu172, Thr186, Leu190, Val191, and Met214.
The structure of Tud11 in complex with sDMA-Aub peptides, together with the structure of human SND1 (TDRD11) bound to sDMA peptides from PIWIL1, uncovered the composition of the sDMA-binding pocket, which consists of a cage of four aromatic residues and an asparagine.
The binding pocket of SMU.440 consists of several conserved aromatic, hydrophobic and acidic residues in orthologous sequences, matching the binding pocket patterns observed in polyketide cyclases and PR10 proteins indicating a potential ability to bind chemically similar classes of ligands.
