Iodine in PDB 4mro: Human Gkrp Bound to Amg-5980 and S6P

The structure of Human Gkrp Bound to Amg-5980 and S6P, PDB code: 4mro was solved by D.J.St Jean, K.S.Ashton, M.D.Bartberger, J.Chen, S.Chmait, R.Cupples, E.Galbreath, J.Helmering, S.R.Jordan, L.Liu, K.Kunz, K.Michelsen, N.Nishimura, L.D.Pennington, S.F.Poon, G.Sivits, M.M.Stec, N.Tamayo, G.Van, K.Yang, M.H.Norman, C.Fotsch, D.J.Lloyd, C.Hale, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.00 / 2.20
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	149.129, 149.129, 132.383, 90.00, 90.00, 120.00
R / Rfree (%)	23 / 28.8

The structure of Human Gkrp Bound to Amg-5980 and S6P also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Iodine atom in the Human Gkrp Bound to Amg-5980 and S6P (pdb code 4mro). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 25 binding sites of Iodine where determined in the Human Gkrp Bound to Amg-5980 and S6P, PDB code: 4mro:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 25 in the Human Gkrp Bound to Amg-5980 and S6P


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-5980 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:I703 b:74.9 occ:1.00 N A:PHE472 3.6 67.6 1.0 CB A:TYR468 3.6 68.8 1.0 N A:ILE473 3.9 60.1 1.0 N A:TYR468 4.0 74.5 1.0 CB A:PHE466 4.1 0.2 1.0 CD2 A:TYR468 4.1 64.1 1.0 CB A:PHE472 4.2 65.2 1.0 CA A:PHE472 4.3 65.4 1.0 CA A:TYR468 4.3 74.5 1.0 C A:ASN471 4.3 67.5 1.0 CG A:TYR468 4.4 68.3 1.0 CG2 A:ILE473 4.4 67.8 1.0 OE1 A:GLU467 4.4 97.3 1.0 CD1 A:LEU275 4.5 54.3 1.0 CB A:ILE473 4.5 68.6 1.0 CA A:PHE466 4.5 96.6 1.0 CA A:ASN471 4.6 78.4 1.0 C A:PHE472 4.6 60.1 1.0 N A:GLU467 4.6 95.2 1.0 ND2 A:ASN471 4.7 85.0 1.0 O A:TYR468 4.7 83.6 1.0 CD2 A:PHE472 4.8 68.2 1.0 C A:TYR468 4.8 86.3 1.0 CA A:ILE473 4.9 54.1 1.0 C A:PHE466 4.9 93.9 1.0 CG A:PHE472 5.0 67.1 1.0 CD2 A:LEU275 5.0 50.0 1.0

Iodine binding site 2 out of 25 in the Human Gkrp Bound to Amg-5980 and S6P


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-5980 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:I704 b:60.1 occ:1.00 CD2 A:LEU506 4.1 58.0 1.0 CA A:CYS598 4.1 58.6 1.0 CG2 A:VAL601 4.3 51.3 1.0 CB A:LEU506 4.3 51.8 1.0 CB A:ASP507 4.4 38.9 1.0 CB A:VAL601 4.4 48.0 1.0 CG1 A:VAL597 4.5 59.2 1.0 N A:CYS598 4.6 59.6 1.0 CG1 A:VAL601 4.6 49.8 1.0 CB A:CYS598 4.6 61.4 1.0 CG A:LEU506 4.8 55.3 1.0 CD2 A:LEU501 4.8 60.3 1.0 SG A:CYS598 4.8 71.3 1.0 C A:VAL597 4.8 57.7 1.0 O A:VAL597 4.9 59.7 1.0 N A:ASP507 4.9 41.5 1.0 O A:LYS499 5.0 55.8 1.0

Iodine binding site 3 out of 25 in the Human Gkrp Bound to Amg-5980 and S6P


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-5980 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:I705 b:51.7 occ:0.80 NH1 A:ARG73 3.6 42.1 1.0 CA A:GLY250 3.8 31.8 1.0 N A:GLY250 4.0 33.3 1.0 CG2 A:ILE30 4.1 43.9 1.0 CD1 A:ILE30 4.3 42.6 1.0 CB A:ALA248 4.4 28.4 1.0 CG1 A:ILE30 4.7 43.3 1.0 CD A:PRO251 4.7 37.6 1.0 CZ A:ARG73 4.8 43.0 1.0 C A:GLY250 5.0 32.2 1.0

Iodine binding site 4 out of 25 in the Human Gkrp Bound to Amg-5980 and S6P


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-5980 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:I706 b:86.4 occ:1.00 N A:ALA46 3.6 55.6 1.0 CD A:LYS318 3.9 73.2 1.0 CD2 A:LEU496 3.9 51.9 1.0 CG A:LYS318 4.0 64.5 1.0 CB A:ALA46 4.1 62.2 1.0 CB A:ASP45 4.2 59.7 1.0 CA A:ASP45 4.4 61.3 1.0 CA A:ALA46 4.5 62.1 1.0 C A:ASP45 4.5 60.1 1.0 CD1 A:LEU496 4.6 55.7 1.0 CG A:LEU496 4.9 54.7 1.0

Iodine binding site 5 out of 25 in the Human Gkrp Bound to Amg-5980 and S6P


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-5980 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:I707 b:65.7 occ:0.85 OG1 A:THR298 3.1 43.8 1.0 O A:GLU294 4.0 43.1 1.0 CB A:THR298 4.1 40.9 1.0 CG1 A:ILE473 4.1 68.5 1.0 C A:GLU294 4.2 45.6 1.0 CG1 A:ILE295 4.2 41.5 1.0 CA A:ILE295 4.2 42.7 1.0 N A:ILE295 4.3 44.5 1.0 CB A:GLU294 4.4 59.5 1.0 CD1 A:ILE473 4.5 69.0 1.0 CG2 A:THR298 4.5 40.3 1.0 OE2 A:GLU294 4.8 86.1 1.0 CB A:ILE295 4.8 42.0 1.0 CD1 A:LEU464 4.9 79.7 1.0 CA A:GLU294 4.9 50.6 1.0

Iodine binding site 6 out of 25 in the Human Gkrp Bound to Amg-5980 and S6P


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-5980 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:I708 b:81.3 occ:0.80 N A:GLY151 3.5 40.0 1.0 C A:ARG149 3.8 40.6 1.0 CA A:ARG149 3.8 48.1 1.0 CA A:GLY151 3.9 42.3 1.0 N A:GLU150 4.1 38.0 1.0 O A:ARG149 4.2 46.6 1.0 CB A:ARG149 4.3 54.3 1.0 C A:GLY151 4.5 44.9 1.0 N A:THR152 4.5 45.3 1.0 CG2 A:THR152 4.6 47.7 1.0 C A:GLU150 4.7 44.3 1.0 CA A:GLU150 4.9 41.3 1.0

Iodine binding site 7 out of 25 in the Human Gkrp Bound to Amg-5980 and S6P


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-5980 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:I709 b:83.9 occ:0.65 N A:GLY3 3.4 68.5 1.0 CA A:GLY3 3.6 65.6 1.0 CG A:ARG6 3.7 56.5 1.0 C A:GLY3 4.0 63.4 1.0 N A:THR4 4.1 57.1 1.0 CG A:LYS5 4.1 84.6 1.0 N A:LYS5 4.1 64.5 1.0 NZ B:LYS235 4.2 78.3 1.0 CB A:ALA554 4.2 46.1 1.0 N A:ARG6 4.2 55.8 1.0 CA A:ALA554 4.4 48.4 1.0 CD A:ARG6 4.5 54.0 1.0 C A:PRO2 4.6 68.8 1.0 O A:MET1 4.6 85.1 1.0 CB A:LYS5 4.6 71.8 1.0 O A:ALA554 4.6 41.7 1.0 O A:GLY3 4.7 58.3 1.0 CA A:LYS5 4.7 69.9 1.0 CB A:ARG6 4.8 53.7 1.0 C A:LYS5 4.9 61.1 1.0 C A:THR4 4.9 56.6 1.0 CA A:PRO2 5.0 74.1 1.0

Iodine binding site 8 out of 25 in the Human Gkrp Bound to Amg-5980 and S6P


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-5980 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:I710 b:61.8 occ:0.50 NH2 A:ARG581 3.5 77.6 1.0 N A:SER530 3.6 49.5 1.0 CB A:GLN529 3.7 55.3 1.0 CA A:GLN529 3.8 50.7 1.0 CG A:GLN529 3.8 56.0 1.0 NE A:ARG533 4.2 63.4 1.0 C A:GLN529 4.2 55.6 1.0 CB A:SER530 4.4 45.2 1.0 CA A:SER530 4.5 51.9 1.0 CD A:ARG533 4.5 58.2 1.0 CZ A:ARG581 4.7 72.9 1.0 CG A:ARG533 4.7 59.3 1.0 CD A:GLN529 4.8 58.1 1.0 OG A:SER530 4.8 44.6 1.0 NE2 A:GLN529 4.9 55.0 1.0 NH1 A:ARG581 5.0 73.4 1.0

Iodine binding site 9 out of 25 in the Human Gkrp Bound to Amg-5980 and S6P


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-5980 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:I711 b:67.1 occ:0.40 OD1 A:ASN196 3.4 62.0 1.0 I B:IOD713 3.7 64.3 0.4 CH2 A:TRP222 3.9 37.3 1.0 CA A:CYS193 3.9 40.0 1.0 CB A:CYS193 4.3 40.5 1.0 CZ2 A:TRP222 4.3 35.3 1.0 CG A:ASN196 4.4 48.2 1.0 N A:CYS193 4.4 36.0 1.0 CB A:ASN196 4.6 48.4 1.0 CH2 B:TRP222 4.8 38.8 1.0 CD1 A:ILE160 4.9 49.5 1.0 SG A:CYS193 5.0 57.9 1.0 C A:ASP192 5.0 38.0 1.0

Iodine binding site 10 out of 25 in the Human Gkrp Bound to Amg-5980 and S6P


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-5980 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:I712 b:88.8 occ:0.60 OG A:SER458 3.1 75.2 1.0 CD1 A:ILE456 3.6 84.5 1.0 CD1 A:LEU445 3.8 86.0 1.0 CG A:LEU445 3.9 87.9 1.0 CB A:ALA437 4.1 73.0 1.0 CB A:SER458 4.2 66.4 1.0 CB A:LEU445 4.3 78.8 1.0 CA A:SER458 4.6 66.2 1.0 CD1 A:LEU412 4.6 69.3 1.0 OG A:SER439 4.7 53.5 1.0 O A:ALA437 4.7 64.0 1.0 CD2 A:LEU412 4.8 67.5 1.0 O A:THR444 4.9 73.5 1.0 CG1 A:ILE456 5.0 86.2 1.0

D.J.St Jean, K.S.Ashton, M.D.Bartberger, J.Chen, S.Chmait, R.Cupples, E.Galbreath, J.Helmering, F.T.Hong, S.R.Jordan, L.Liu, R.K.Kunz, K.Michelsen, N.Nishimura, L.D.Pennington, S.F.Poon, D.Reid, G.Sivits, M.M.Stec, S.Tadesse, N.Tamayo, G.Van, K.C.Yang, J.Zhang, M.H.Norman, C.Fotsch, D.J.Lloyd, C.Hale. Small Molecule Disruptors of the Glucokinase-Glucokinase Regulatory Protein Interaction: 2. Leveraging Structure-Based Drug Design to Identify Analogues with Improved Pharmacokinetic Profiles. J.Med.Chem. V. 57 325 2014.
ISSN: ISSN 0022-2623
PubMed: 24405213
DOI: 10.1021/JM4016747