Iodine in PDB 4pxs: Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate

The structure of Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate, PDB code: 4pxs was solved by S.R.Jordan, S.Chmait, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.00 / 2.60
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	148.630, 148.630, 133.622, 90.00, 90.00, 120.00
R / Rfree (%)	23.4 / 30.7

The structure of Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Iodine atom in the Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate (pdb code 4pxs). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 29 binding sites of Iodine where determined in the Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate, PDB code: 4pxs:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 29 in the Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) 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 Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I703 b:84.5 occ:0.95 N A:TYR468 3.7 0.9 1.0 N A:PHE472 3.8 83.0 1.0 CG2 A:ILE473 3.9 93.1 1.0 N A:ILE473 3.9 74.5 1.0 N A:GLU467 4.0 0.8 1.0 CB A:TYR468 4.1 91.9 1.0 CD2 A:TYR468 4.1 79.2 1.0 CB A:ILE473 4.3 88.1 1.0 CB A:GLU467 4.4 0.9 1.0 CB A:PHE472 4.4 76.3 1.0 C A:ASN471 4.4 91.2 1.0 CD2 A:PHE472 4.4 74.0 1.0 CA A:ASN471 4.4 0.1 1.0 CA A:TYR468 4.5 97.8 1.0 CD1 A:LEU275 4.5 68.0 1.0 CA A:PHE472 4.5 79.2 1.0 CA A:GLU467 4.6 0.8 1.0 C A:GLU467 4.6 0.6 1.0 CG A:TYR468 4.6 90.9 1.0 CD2 A:LEU275 4.7 70.0 1.0 C A:PHE472 4.7 76.8 1.0 ND2 A:ASN471 4.8 86.5 1.0 CA A:ILE473 4.8 77.2 1.0 CB A:PHE466 4.9 0.3 1.0 CG A:PHE472 4.9 79.2 1.0 C A:PHE466 5.0 0.3 1.0 N A:ASN471 5.0 0.2 1.0 O A:TYR468 5.0 97.4 1.0

Iodine binding site 2 out of 29 in the Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) 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 Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I704 b:74.8 occ:1.00 CA A:CYS598 4.1 89.9 1.0 CG2 A:VAL601 4.2 62.6 1.0 N A:CYS598 4.3 80.1 1.0 CB A:LEU506 4.3 56.9 1.0 CB A:VAL601 4.4 67.5 1.0 CG1 A:VAL597 4.4 68.1 1.0 CD2 A:LEU506 4.6 59.6 1.0 C A:VAL597 4.6 68.6 1.0 O A:VAL597 4.6 69.7 1.0 CB A:ASP507 4.6 40.4 1.0 CG1 A:VAL601 4.7 71.9 1.0 CD2 A:LEU501 4.8 72.8 1.0 CB A:CYS598 4.9 94.3 1.0 O A:LYS499 4.9 62.5 1.0

Iodine binding site 3 out of 29 in the Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) 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 Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I705 b:64.9 occ:0.65 NH1 A:ARG73 3.6 46.2 1.0 O A:HOH807 3.7 50.1 1.0 CA A:GLY250 3.8 38.6 1.0 N A:GLY250 4.1 36.3 1.0 CG2 A:ILE30 4.2 47.2 1.0 CB A:ALA248 4.2 43.4 1.0 CD1 A:ILE30 4.3 46.9 1.0 CG1 A:ILE30 4.6 44.6 1.0 CZ A:ARG73 4.7 45.8 1.0 CD A:PRO251 4.7 42.2 1.0 NH2 A:ARG73 4.9 46.8 1.0 C A:GLY250 5.0 43.8 1.0

Iodine binding site 4 out of 29 in the Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) 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 Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I706 b:99.8 occ:0.90 N A:ALA46 3.6 77.3 1.0 CB A:ALA46 3.7 75.6 1.0 CG A:LYS318 3.8 85.6 1.0 CD2 A:LEU496 3.8 60.8 1.0 CD A:LYS318 4.1 91.6 1.0 CA A:ALA46 4.3 73.6 1.0 CB A:ASP45 4.4 90.2 1.0 CA A:ASP45 4.4 82.4 1.0 C A:ASP45 4.5 79.2 1.0 CD1 A:LEU496 5.0 58.0 1.0 CG A:LEU496 5.0 62.6 1.0

Iodine binding site 5 out of 29 in the Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) 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 Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I707 b:66.9 occ:0.75 OG1 A:THR298 3.3 55.0 1.0 CB A:GLU294 4.2 77.5 1.0 C A:GLU294 4.2 58.9 1.0 O A:GLU294 4.2 54.0 1.0 CG1 A:ILE295 4.2 66.2 1.0 CA A:ILE295 4.3 55.6 1.0 N A:ILE295 4.3 55.2 1.0 CD1 A:ILE473 4.3 94.0 1.0 CG1 A:ILE473 4.3 88.7 1.0 CD1 A:LEU464 4.4 0.5 1.0 CB A:THR298 4.4 59.8 1.0 CG2 A:THR298 4.8 62.5 1.0 CA A:GLU294 4.8 67.5 1.0 NZ A:LYS279 4.9 80.5 1.0 CB A:ILE295 4.9 63.2 1.0

Iodine binding site 6 out of 29 in the Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) 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 Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I708 b:98.7 occ:0.80 N A:GLY151 3.5 49.1 1.0 C A:ARG149 3.8 52.4 1.0 CA A:GLY151 3.8 49.2 1.0 CA A:ARG149 3.9 55.1 1.0 O A:ARG149 4.0 53.0 1.0 N A:GLU150 4.0 49.8 1.0 CB A:ARG149 4.4 60.1 1.0 N A:THR152 4.4 49.8 1.0 C A:GLY151 4.5 46.4 1.0 C A:GLU150 4.6 50.3 1.0 CG2 A:THR152 4.7 58.6 1.0 CA A:GLU150 4.9 47.9 1.0 CE1 A:HIS565 4.9 61.5 1.0 O A:HOH817 4.9 42.2 1.0 NE2 A:HIS565 4.9 66.3 1.0 CG A:ARG149 4.9 66.0 1.0

Iodine binding site 7 out of 29 in the Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) 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 Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I709 b:98.9 occ:0.60 N A:GLY3 3.4 97.9 1.0 CA A:GLY3 3.7 92.2 1.0 CB A:LYS5 3.7 0.9 1.0 N A:LYS5 3.7 87.0 1.0 N A:ARG6 3.8 70.6 1.0 N A:THR4 3.9 93.2 1.0 CG A:ARG6 4.0 65.6 1.0 CG A:LYS5 4.0 0.1 1.0 C A:GLY3 4.1 92.8 1.0 CA A:LYS5 4.1 93.2 1.0 CB A:ALA554 4.2 54.5 1.0 CA A:ALA554 4.3 56.1 1.0 C A:LYS5 4.5 82.2 1.0 C A:PRO2 4.5 0.7 1.0 CB A:ARG6 4.5 68.3 1.0 C A:THR4 4.6 89.1 1.0 NE A:ARG6 4.7 72.4 1.0 CA A:ARG6 4.7 68.3 1.0 O A:ALA554 4.8 59.0 1.0 CA A:PRO2 4.9 0.6 1.0 CA A:THR4 4.9 92.0 1.0 CD A:ARG6 5.0 63.5 1.0

Iodine binding site 8 out of 29 in the Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) 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 Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I710 b:0.7 occ:0.50 OE2 A:GLU25 3.3 68.1 1.0 CG A:LYS33 3.7 48.9 1.0 N A:SER34 3.8 51.5 1.0 NH2 A:ARG525 3.9 53.6 1.0 CD A:GLU25 3.9 64.7 1.0 CB A:LYS33 4.0 46.6 1.0 CD A:LYS33 4.1 49.7 1.0 CG A:GLU25 4.1 62.7 1.0 CA A:LYS33 4.2 47.0 1.0 CG2 A:VAL28 4.2 44.4 1.0 CB A:SER34 4.2 51.6 1.0 C16 A:2Y6701 4.3 46.8 1.0 O A:SER34 4.3 55.1 1.0 CB A:VAL28 4.4 44.4 1.0 CG1 A:VAL28 4.4 40.0 1.0 CA A:SER34 4.5 54.2 1.0 C A:LYS33 4.5 47.5 1.0 CZ A:ARG525 4.8 54.3 1.0 OE1 A:GLU25 4.8 64.4 1.0 C A:SER34 4.9 52.8 1.0

Iodine binding site 9 out of 29 in the Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) 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 Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I711 b:84.1 occ:0.40 CE A:LYS531 3.4 51.3 1.0 NZ A:LYS531 3.7 56.3 1.0 O A:GLY3 3.8 92.6 1.0 O A:PHE7 3.8 56.6 1.0 OG1 A:THR4 3.9 75.4 1.0 CA A:THR4 3.9 92.0 1.0 O A:THR4 3.9 98.5 1.0 CB A:PHE7 4.0 51.8 1.0 C A:PHE7 4.0 53.1 1.0 C A:THR4 4.4 89.1 1.0 CB A:THR4 4.4 93.4 1.0 N A:GLN8 4.5 56.7 1.0 CA A:GLN8 4.6 60.5 1.0 CA A:PHE7 4.6 51.0 1.0 C A:GLY3 4.7 92.8 1.0 CD A:LYS531 4.8 51.7 1.0 N A:THR4 4.8 93.2 1.0 CG2 A:THR4 4.9 94.4 1.0

Iodine binding site 10 out of 29 in the Human Gkrp Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) 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 Bound to Amg-0265 (N-[(R)-(2-Chlorophenyl){7-[4-(2- Hydroxypropan-2-Yl) Pyridin-2-Yl]-1-Benzothiophen-2- Yl}Methyl]Cyclopropanesulfonamide) and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:I712 b:92.2 occ:0.50 OD1 A:ASN196 3.3 78.1 1.0 NZ A:LYS164 3.9 90.4 1.0 CA A:CYS193 4.0 54.8 1.0 CB A:CYS193 4.2 60.8 1.0 CG A:ASN196 4.2 64.6 1.0 SG A:CYS193 4.5 69.5 1.0 CB A:ASN196 4.5 69.9 1.0 I B:IOD714 4.6 94.0 0.5 CD1 A:ILE160 4.8 46.4 1.0 N A:CYS193 4.8 52.0 1.0 O A:CYS193 4.8 57.5 1.0 CH2 A:TRP222 4.9 70.5 1.0 C A:CYS193 4.9 59.5 1.0

L.D.Pennington, M.D.Bartberger, M.D.Croghan, K.L.Andrews, K.S.Ashton, M.P.Bourbeau, J.Chen, S.Chmait, R.Cupples, C.Fotsch. Discovery and Structure-Guided Optimization of Diarylmethanesulfonamide Disruptors of Gk-Gkrp Binding. To Be Published.