Table 4

Defining a minimal GPCR pocket
B1 B2 B3 B4 B5 B6 B7
M1, G3, L31, Q36, F37, M44, M86, G90, T93, T94, T97, S98, F103, E113, G114, A117, T118, G121, E122, L125, P171, L172, Y178, I179, P180, E181, S186, C187, G188, I189, Y191, T193, P194, H195, E196, E197, N200, F203, V204, M207, F208, H211, F212, F261, W265, Y268, A269, A272, F273, I275, H278, Q279, S281, F283, P285, M288, T289, A292, F293, A295, K296 M86, T94, T97, S98, F103, E113, G114, A117, T118, G121, E122, L125, Y178, I179, P180, E181, S186, C187, G188, I189, Y191, F203, V204, M207, F208, H211, F212, F261, W265, Y268, A269, A272, P285, M288, T289, A292, F293, K296 T94, T97, S98, E113, G114, A117, T118, G121, E122, Y178, I179, P180, E181, G188, I189, Y191, F203, V204, M207, F208, H211, W265, Y268, A269, A272, P285, M288, T289, A292, F293, K296 T94, E113, G114, A117, T118, G121, E122, P180, I189, F203, V204, M207, F208, H211, W265, Y268, A269, A272, M288, T289, A292, K296 E113, G114, A117, T118, G121, E122, P180, I189, M207, F208, H211, W265, Y268, A269, A272, M288, A292, K296 E113, G114, A117, T118, M207, W265, Y268, A269, A272, A292 T118, M207, Y268, A292
61 38 31 22 18 10 4

The residues listed are analogous binding pockets mapped onto the rhodopsin structure (1U19). The binding pockets are arranged in the order of decreasing size of the binding pocket (left to right). The numbers in the last row represent the number residues in the binding pocket. B1, B2, B3, B4, B5, B6 and B7 represent common sets of residues present in at least one, two, three, four, five, six and seven known receptor ligand binding pockets, respectively.

Moitra et al.

Moitra et al. BMC Biophysics 2012 5:13   doi:10.1186/2046-1682-5-13

Open Data