Fluorine in PDB 4ohk: Human Gkrp Bound to Amg-2526 and S6P

The structure of Human Gkrp Bound to Amg-2526 and S6P, PDB code: 4ohk 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)	29.72 / 2.80
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	149.590, 149.590, 132.651, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 28.3

The structure of Human Gkrp Bound to Amg-2526 and S6P also contains other interesting chemical elements:

Iodine

(I)

25 atoms

The binding sites of Fluorine atom in the Human Gkrp Bound to Amg-2526 and S6P (pdb code 4ohk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human Gkrp Bound to Amg-2526 and S6P, PDB code: 4ohk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Human Gkrp Bound to Amg-2526 and S6P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Gkrp Bound to Amg-2526 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:48.5 occ:1.00 F2 A:2TE701 0.0 48.5 1.0 C24 A:2TE701 1.3 51.7 1.0 F3 A:2TE701 2.2 59.0 1.0 F1 A:2TE701 2.3 55.2 1.0 C12 A:2TE701 2.3 46.6 1.0 C20 A:2TE701 2.8 42.1 1.0 O A:GLU32 2.8 38.6 1.0 C9 A:2TE701 2.9 42.3 1.0 C10 A:2TE701 3.0 43.5 1.0 C21 A:2TE701 3.4 43.7 1.0 CE1 A:HIS504 3.5 47.4 1.0 O3 A:2TE701 3.6 43.6 1.0 C A:GLU32 3.9 40.1 1.0 N A:SER34 4.1 53.3 1.0 ND1 A:HIS504 4.1 50.1 1.0 C A:LYS33 4.1 47.4 1.0 C8 A:2TE701 4.1 39.2 1.0 C11 A:2TE701 4.3 44.9 1.0 CA A:LYS33 4.3 46.7 1.0 C22 A:2TE701 4.3 53.5 1.0 O A:LYS33 4.5 45.1 1.0 NE2 A:HIS504 4.6 47.4 1.0 CB A:SER255 4.6 43.8 1.0 N A:LYS33 4.6 39.9 1.0 CB A:SER34 4.6 52.6 1.0 CA A:SER34 4.7 52.6 1.0 CG1 A:VAL28 4.8 40.5 1.0 OG A:SER255 4.9 47.1 1.0 NH2 A:ARG525 4.9 65.3 1.0

Fluorine binding site 2 out of 6 in the Human Gkrp Bound to Amg-2526 and S6P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Gkrp Bound to Amg-2526 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:59.0 occ:1.00 F3 A:2TE701 0.0 59.0 1.0 C24 A:2TE701 1.3 51.7 1.0 F1 A:2TE701 2.2 55.2 1.0 F2 A:2TE701 2.2 48.5 1.0 C12 A:2TE701 2.3 46.6 1.0 C21 A:2TE701 2.5 43.7 1.0 O3 A:2TE701 2.7 43.6 1.0 C20 A:2TE701 2.9 42.1 1.0 C22 A:2TE701 3.0 53.5 1.0 NE A:ARG525 3.3 62.9 1.0 NH2 A:ARG525 3.3 65.3 1.0 CE1 A:HIS504 3.4 47.4 1.0 CZ A:ARG525 3.6 62.9 1.0 C9 A:2TE701 3.7 42.3 1.0 NE2 A:HIS504 3.9 47.4 1.0 C23 A:2TE701 4.0 57.3 1.0 CD A:ARG525 4.4 65.1 1.0 CB A:SER34 4.4 52.6 1.0 ND1 A:HIS504 4.4 50.1 1.0 C10 A:2TE701 4.4 43.5 1.0 CG A:ARG525 4.5 63.7 1.0 C8 A:2TE701 4.6 39.2 1.0 N A:SER34 4.8 53.3 1.0 O A:HOH801 4.8 54.1 1.0 CB A:ARG525 4.8 60.9 1.0 NH1 A:ARG525 4.9 63.2 1.0 O A:GLU32 4.9 38.6 1.0 I A:IOD710 5.0 0.3 0.5

Fluorine binding site 3 out of 6 in the Human Gkrp Bound to Amg-2526 and S6P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Gkrp Bound to Amg-2526 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:55.2 occ:1.00 F1 A:2TE701 0.0 55.2 1.0 C24 A:2TE701 1.3 51.7 1.0 F3 A:2TE701 2.2 59.0 1.0 C12 A:2TE701 2.2 46.6 1.0 F2 A:2TE701 2.3 48.5 1.0 O3 A:2TE701 2.6 43.6 1.0 C9 A:2TE701 2.8 42.3 1.0 NH2 A:ARG525 3.0 65.3 1.0 C8 A:2TE701 3.4 39.2 1.0 C20 A:2TE701 3.5 42.1 1.0 CG1 A:VAL28 3.6 40.5 1.0 C10 A:2TE701 3.7 43.5 1.0 CG2 A:VAL28 3.9 42.0 1.0 I A:IOD710 3.9 0.3 0.5 C21 A:2TE701 4.0 43.7 1.0 CZ A:ARG525 4.0 62.9 1.0 O A:GLU32 4.1 38.6 1.0 NE A:ARG525 4.2 62.9 1.0 CB A:VAL28 4.3 41.3 1.0 CA A:LYS33 4.5 46.7 1.0 C7 A:2TE701 4.5 41.0 1.0 N A:SER34 4.6 53.3 1.0 OE2 A:GLU25 4.6 69.1 1.0 O A:HOH801 4.7 54.1 1.0 C A:GLU32 4.8 40.1 1.0 C22 A:2TE701 4.8 53.5 1.0 C11 A:2TE701 4.8 44.9 1.0 C A:LYS33 4.8 47.4 1.0 N A:LYS33 5.0 39.9 1.0

Fluorine binding site 4 out of 6 in the Human Gkrp Bound to Amg-2526 and S6P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Gkrp Bound to Amg-2526 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:49.9 occ:1.00 F2 B:2TE701 0.0 49.9 1.0 C24 B:2TE701 1.3 53.2 1.0 F3 B:2TE701 2.1 62.4 1.0 F1 B:2TE701 2.2 59.3 1.0 C12 B:2TE701 2.4 48.4 1.0 O3 B:2TE701 2.7 47.5 1.0 NH2 B:ARG525 2.8 53.1 1.0 C21 B:2TE701 3.0 44.0 1.0 NE B:ARG525 3.1 48.7 1.0 CZ B:ARG525 3.2 50.5 1.0 C20 B:2TE701 3.2 44.7 1.0 C22 B:2TE701 3.3 51.2 1.0 C9 B:2TE701 3.7 43.2 1.0 CE1 B:HIS504 3.9 34.9 1.0 I B:IOD711 4.0 0.9 0.5 CD B:ARG525 4.3 48.3 1.0 NE2 B:HIS504 4.3 35.0 1.0 C23 B:2TE701 4.3 59.1 1.0 NH1 B:ARG525 4.4 49.0 1.0 N B:SER34 4.4 38.4 1.0 CB B:SER34 4.4 40.2 1.0 C8 B:2TE701 4.5 41.9 1.0 C10 B:2TE701 4.7 42.1 1.0 CG B:ARG525 4.9 51.4 1.0 O B:GLU32 4.9 33.8 1.0 O B:HOH801 5.0 41.8 1.0

Fluorine binding site 5 out of 6 in the Human Gkrp Bound to Amg-2526 and S6P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Gkrp Bound to Amg-2526 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:62.4 occ:1.00 F3 B:2TE701 0.0 62.4 1.0 C24 B:2TE701 1.3 53.2 1.0 F2 B:2TE701 2.1 49.9 1.0 F1 B:2TE701 2.2 59.3 1.0 C12 B:2TE701 2.3 48.4 1.0 C9 B:2TE701 2.7 43.2 1.0 O3 B:2TE701 3.0 47.5 1.0 C8 B:2TE701 3.2 41.9 1.0 O B:GLU32 3.3 33.8 1.0 CG1 B:VAL28 3.4 40.2 1.0 C20 B:2TE701 3.6 44.7 1.0 C10 B:2TE701 3.6 42.1 1.0 NH2 B:ARG525 3.7 53.1 1.0 CA B:LYS33 3.8 38.9 1.0 I B:IOD711 3.9 0.9 0.5 N B:SER34 3.9 38.4 1.0 C B:GLU32 4.0 35.1 1.0 C21 B:2TE701 4.1 44.0 1.0 C B:LYS33 4.2 37.1 1.0 CG2 B:VAL28 4.2 34.1 1.0 N B:LYS33 4.3 36.2 1.0 C7 B:2TE701 4.3 42.8 1.0 CB B:VAL28 4.4 37.1 1.0 C11 B:2TE701 4.6 41.2 1.0 CZ B:ARG525 4.7 50.5 1.0 O B:HOH852 4.7 47.7 1.0 C22 B:2TE701 4.8 51.2 1.0 NE B:ARG525 4.9 48.7 1.0 CE1 B:HIS504 4.9 34.9 1.0 CB B:GLU32 4.9 36.2 1.0 C6 B:2TE701 4.9 40.7 1.0 CB B:LYS33 5.0 44.1 1.0

Fluorine binding site 6 out of 6 in the Human Gkrp Bound to Amg-2526 and S6P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Gkrp Bound to Amg-2526 and S6P within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:59.3 occ:1.00 F1 B:2TE701 0.0 59.3 1.0 C24 B:2TE701 1.3 53.2 1.0 F3 B:2TE701 2.2 62.4 1.0 F2 B:2TE701 2.2 49.9 1.0 C12 B:2TE701 2.4 48.4 1.0 C20 B:2TE701 2.7 44.7 1.0 C21 B:2TE701 2.8 44.0 1.0 CE1 B:HIS504 2.9 34.9 1.0 C9 B:2TE701 3.2 43.2 1.0 C8 B:2TE701 3.2 41.9 1.0 C22 B:2TE701 3.4 51.2 1.0 O B:GLU32 3.5 33.8 1.0 O3 B:2TE701 3.6 47.5 1.0 ND1 B:HIS504 3.6 36.7 1.0 NE2 B:HIS504 3.9 35.0 1.0 O B:HOH852 4.1 47.7 1.0 N B:SER34 4.2 38.4 1.0 C10 B:2TE701 4.5 42.1 1.0 C7 B:2TE701 4.5 42.8 1.0 CB B:SER255 4.5 39.9 1.0 C23 B:2TE701 4.6 59.1 1.0 C B:LYS33 4.6 37.1 1.0 OG B:SER255 4.6 45.3 1.0 C B:GLU32 4.7 35.1 1.0 CB B:SER34 4.7 40.2 1.0 CG B:HIS504 4.8 34.9 1.0 CA B:SER34 4.8 39.8 1.0 NH2 B:ARG525 4.8 53.1 1.0 CA B:LYS33 4.9 38.9 1.0 CD2 B:HIS504 4.9 34.2 1.0 NE B:ARG525 5.0 48.7 1.0

N.Nishimura, M.H.Norman, L.Liu, K.C.Yang, K.S.Ashton, M.D.Bartberger, S.Chmait, J.Chen, R.Cupples, C.Fotsch, J.Helmering, S.R.Jordan, R.K.Kunz, L.D.Pennington, S.F.Poon, A.Siegmund, G.Sivits, D.J.Lloyd, C.Hale, D.J.St Jean. Small Molecule Disruptors of the Glucokinase-Glucokinase Regulatory Protein Interaction: 3. Structure-Activity Relationships Within the Aryl Carbinol Region of the N-Arylsulfonamido-N'-Arylpiperazine Series. J.Med.Chem. V. 57 3094 2014.
ISSN: ISSN 0022-2623
PubMed: 24611879
DOI: 10.1021/JM5000497