Iodine in PDB 4ly9: Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate

The structure of Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate, PDB code: 4ly9 was solved by S.R.Jordan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.87 / 2.35
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	148.869, 148.869, 132.397, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 27

The structure of Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Iodine atom in the Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate (pdb code 4ly9). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 26 binding sites of Iodine where determined in the Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate, PDB code: 4ly9:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 26 in the Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I701 b:70.1 occ:1.00 N A:PHE472 3.6 56.4 1.0 CB A:TYR468 3.7 75.0 1.0 N A:ILE473 3.9 50.5 1.0 CB A:PHE466 4.1 0.4 1.0 CB A:PHE472 4.1 57.3 1.0 N A:TYR468 4.1 77.7 1.0 CD2 A:TYR468 4.2 62.2 1.0 CA A:PHE472 4.3 57.2 1.0 CD1 A:LEU275 4.3 50.0 1.0 CA A:TYR468 4.4 77.8 1.0 OE1 A:GLU467 4.4 82.5 1.0 C A:ASN471 4.4 61.0 1.0 CG A:TYR468 4.4 72.9 1.0 CA A:ASN471 4.5 70.2 1.0 CA A:PHE466 4.6 97.9 1.0 CB A:ILE473 4.6 58.4 1.0 CD2 A:PHE472 4.6 65.2 1.0 C A:PHE472 4.6 51.5 1.0 ND2 A:ASN471 4.6 75.5 1.0 O A:TYR468 4.7 84.9 1.0 N A:GLU467 4.8 98.4 1.0 C A:TYR468 4.9 86.4 1.0 CG A:PHE472 4.9 63.5 1.0 CA A:ILE473 4.9 45.9 1.0 CD2 A:LEU275 4.9 45.7 1.0 C A:PHE466 5.0 96.0 1.0

Iodine binding site 2 out of 26 in the Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I702 b:50.6 occ:0.90 CD2 A:LEU506 4.0 49.7 1.0 CA A:CYS598 4.1 60.4 1.0 CG2 A:VAL601 4.3 51.0 1.0 CB A:LEU506 4.3 46.4 1.0 CB A:VAL601 4.4 51.6 1.0 N A:CYS598 4.4 60.9 1.0 CG1 A:VAL597 4.5 53.6 1.0 CB A:ASP507 4.5 31.7 1.0 CG1 A:VAL601 4.6 50.6 1.0 CB A:CYS598 4.6 68.2 1.0 SG A:CYS598 4.7 76.0 1.0 CD2 A:LEU501 4.7 53.5 1.0 C A:VAL597 4.7 57.0 1.0 O A:VAL597 4.8 58.2 1.0 CG A:LEU506 4.8 50.3 1.0 CB A:LEU501 5.0 47.4 1.0 CD1 A:LEU501 5.0 54.4 1.0 N A:ASP507 5.0 36.6 1.0 CG A:PRO572 5.0 37.3 1.0

Iodine binding site 3 out of 26 in the Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I703 b:39.4 occ:0.60 NH1 A:ARG73 3.5 36.4 1.0 O A:HOH815 3.8 39.2 1.0 CA A:GLY250 3.9 26.9 1.0 CG2 A:ILE30 4.1 33.1 1.0 N A:GLY250 4.2 26.5 1.0 CD1 A:ILE30 4.2 35.8 1.0 CB A:ALA248 4.3 24.2 1.0 CD A:PRO251 4.6 28.4 1.0 CG1 A:ILE30 4.6 32.4 1.0 CZ A:ARG73 4.7 35.6 1.0 NH2 A:ARG73 5.0 29.2 1.0

Iodine binding site 4 out of 26 in the Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I704 b:72.5 occ:0.80 N A:ALA46 3.6 45.1 1.0 CD A:LYS318 3.8 82.6 1.0 CG A:LYS318 3.9 70.5 1.0 CB A:ALA46 3.9 47.7 1.0 CD2 A:LEU496 4.0 52.4 1.0 CA A:ALA46 4.4 51.2 1.0 CB A:ASP45 4.4 56.7 1.0 CA A:ASP45 4.5 55.8 1.0 C A:ASP45 4.5 52.0 1.0 CD1 A:LEU496 4.7 53.0 1.0 CG A:LEU496 4.9 52.2 1.0

Iodine binding site 5 out of 26 in the Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I705 b:46.4 occ:0.60 OG1 A:THR298 3.3 36.0 1.0 O A:GLU294 4.0 43.8 1.0 CG1 A:ILE473 4.0 55.4 1.0 CB A:THR298 4.1 35.0 1.0 CG1 A:ILE295 4.1 34.6 1.0 C A:GLU294 4.2 39.4 1.0 CA A:ILE295 4.2 35.9 1.0 N A:ILE295 4.3 38.0 1.0 CB A:GLU294 4.5 51.7 1.0 CD1 A:ILE473 4.5 54.9 1.0 CG2 A:THR298 4.5 36.5 1.0 CD1 A:LEU464 4.7 98.9 1.0 CB A:ILE295 4.8 35.5 1.0 O A:HOH854 4.9 36.1 1.0 OE2 A:GLU294 4.9 74.2 1.0 NZ A:LYS279 4.9 66.2 1.0 CA A:GLU294 5.0 44.5 1.0

Iodine binding site 6 out of 26 in the Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I706 b:53.9 occ:0.60 N A:GLY151 3.5 37.5 1.0 CA A:GLY151 3.8 37.2 1.0 C A:ARG149 3.8 37.9 1.0 CA A:ARG149 3.9 44.2 1.0 N A:GLU150 4.1 38.5 1.0 O A:ARG149 4.2 41.2 1.0 CB A:ARG149 4.2 51.3 1.0 C A:GLY151 4.5 39.0 1.0 N A:THR152 4.5 38.0 1.0 CG2 A:THR152 4.5 37.3 1.0 C A:GLU150 4.7 40.1 1.0 O A:HOH806 4.8 42.8 1.0 CG A:ARG149 4.9 57.9 1.0

Iodine binding site 7 out of 26 in the Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I707 b:82.0 occ:0.60 N A:GLY3 3.4 59.5 1.0 CB A:LYS5 3.5 77.1 1.0 N A:LYS5 3.6 65.3 1.0 CA A:GLY3 3.7 56.9 1.0 CG A:ARG6 3.7 49.4 1.0 C A:GLY3 3.9 59.1 1.0 CA A:LYS5 4.0 71.3 1.0 N A:ARG6 4.1 53.7 1.0 N A:THR4 4.1 54.5 1.0 CB A:ALA554 4.3 39.8 1.0 CA A:ALA554 4.3 40.9 1.0 C A:PRO2 4.5 63.1 1.0 CD A:ARG6 4.5 50.0 1.0 O A:MET1 4.5 71.1 1.0 O A:GLY3 4.5 55.4 1.0 C A:LYS5 4.5 60.2 1.0 O A:ALA554 4.6 37.2 1.0 C A:THR4 4.7 61.5 1.0 CA A:PRO2 4.7 68.8 1.0 CG A:LYS5 4.8 91.9 1.0 CB A:ARG6 4.9 49.4 1.0 C A:ALA554 5.0 37.5 1.0 CA A:THR4 5.0 58.8 1.0

Iodine binding site 8 out of 26 in the Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I708 b:82.8 occ:0.55 CA A:CYS193 3.9 39.1 1.0 OD1 A:ASN196 3.9 54.5 1.0 I B:IOD709 4.0 74.1 0.5 CB A:CYS193 4.1 42.1 1.0 CH2 A:TRP222 4.2 36.3 1.0 SG A:CYS193 4.4 55.0 1.0 O B:HOH863 4.6 45.8 1.0 N A:CYS193 4.7 36.1 1.0 CZ2 A:TRP222 4.7 33.7 1.0 CB A:ASN196 4.8 50.1 1.0 CG A:ASN196 4.8 45.0 1.0 CD1 A:ILE160 5.0 42.1 1.0

Iodine binding site 9 out of 26 in the Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I709 b:78.4 occ:0.80 N A:SER530 3.7 43.2 1.0 CA A:GLN529 3.8 45.3 1.0 NH2 A:ARG581 3.8 70.3 1.0 CB A:GLN529 3.8 48.9 1.0 CD A:ARG533 3.9 54.3 1.0 CG A:GLN529 4.2 52.7 1.0 C A:GLN529 4.2 47.9 1.0 NE A:ARG533 4.3 63.5 1.0 CB A:SER530 4.4 37.9 1.0 OG A:SER530 4.6 41.8 1.0 CA A:SER530 4.6 41.3 1.0 NE2 A:GLN529 4.9 53.4 1.0 CD A:GLN529 4.9 52.0 1.0 CZ A:ARG581 5.0 66.3 1.0

Iodine binding site 10 out of 26 in the Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Human Gkrp Complexed to Amg-1694 [(2R)-1,1,1-Trifluoro-2-{4-[(2S)-2- {[(3S)-3-Methylmorpholin-4-Yl]Methyl}-4-(Thiophen-2-Ylsulfonyl) Piperazin-1-Yl]Phenyl}Propan-2-Ol] and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I710 b:62.9 occ:0.50 O A:HOH855 3.1 35.8 1.0 N A:GLU77 3.9 34.6 1.0 CA A:SER76 4.0 33.5 1.0 OE1 A:GLU64 4.0 46.4 1.0 CB A:SER76 4.2 31.9 1.0 C A:SER76 4.5 34.9 1.0 OG A:SER76 4.5 34.7 1.0 CD A:GLU64 4.8 53.4 1.0 O A:HOH830 4.8 37.8 1.0 CB A:GLU77 4.8 45.7 1.0 CB A:GLU64 4.9 55.8 1.0 CA A:GLU77 4.9 38.1 1.0

D.J.Lloyd, D.J.St Jean, R.J.Kurzeja, R.C.Wahl, K.Michelsen, R.Cupples, M.Chen, J.Wu, G.Sivits, J.Helmering, R.Komorowski, K.S.Ashton, L.D.Pennington, C.Fotsch, M.Vazir, K.Chen, S.Chmait, J.Zhang, L.Liu, M.H.Norman, K.L.Andrews, M.D.Bartberger, G.Van, E.J.Galbreath, S.L.Vonderfecht, M.Wang, S.R.Jordan, M.M.Veniant, C.Hale. Antidiabetic Effects of Glucokinase Regulatory Protein Small-Molecule Disruptors. Nature V. 504 437 2013.
ISSN: ISSN 0028-0836
PubMed: 24226772
DOI: 10.1038/NATURE12724