Fluorine in PDB 4ohm: Human Gkrp Bound to Amg-0771 and Sorbitol-6-Phosphate

The structure of Human Gkrp Bound to Amg-0771 and Sorbitol-6-Phosphate, PDB code: 4ohm 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)	37.97 / 2.40
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	149.181, 149.181, 132.327, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 27.2

The structure of Human Gkrp Bound to Amg-0771 and Sorbitol-6-Phosphate also contains other interesting chemical elements:

Iodine

(I)

24 atoms

The binding sites of Fluorine atom in the Human Gkrp Bound to Amg-0771 and Sorbitol-6-Phosphate (pdb code 4ohm). 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-0771 and Sorbitol-6-Phosphate, PDB code: 4ohm:
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-0771 and Sorbitol-6-Phosphate


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-0771 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:40.6 occ:1.00 F2 A:2TF701 0.0 40.6 1.0 C21 A:2TF701 1.3 40.4 1.0 F1 A:2TF701 2.1 38.1 1.0 C12 A:2TF701 2.3 37.2 1.0 F3 A:2TF701 2.3 41.3 1.0 O3 A:2TF701 2.7 33.2 1.0 C9 A:2TF701 2.8 34.6 1.0 CG1 A:VAL28 3.3 36.0 1.0 C10 A:2TF701 3.3 35.8 1.0 NH2 A:ARG525 3.4 42.3 1.0 C20 A:2TF701 3.6 37.1 1.0 C8 A:2TF701 3.7 37.1 1.0 CG2 A:VAL28 3.8 36.8 1.0 O A:GLU32 3.9 33.8 1.0 O4 A:2TF701 4.0 45.2 1.0 CB A:VAL28 4.0 37.6 1.0 CA A:LYS33 4.1 38.0 1.0 N A:SER34 4.2 38.9 1.0 C11 A:2TF701 4.5 33.5 1.0 CZ A:ARG525 4.5 41.9 1.0 C A:GLU32 4.5 32.4 1.0 C A:LYS33 4.6 39.0 1.0 NE A:ARG525 4.7 45.9 1.0 C7 A:2TF701 4.7 36.9 1.0 OE2 A:GLU25 4.7 65.1 1.0 N A:LYS33 4.7 34.8 1.0 CG A:LYS33 5.0 35.1 1.0

Fluorine binding site 2 out of 6 in the Human Gkrp Bound to Amg-0771 and Sorbitol-6-Phosphate


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-0771 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:41.3 occ:1.00 F3 A:2TF701 0.0 41.3 1.0 C21 A:2TF701 1.4 40.4 1.0 F1 A:2TF701 2.2 38.1 1.0 F2 A:2TF701 2.3 40.6 1.0 C12 A:2TF701 2.3 37.2 1.0 C20 A:2TF701 2.8 37.1 1.0 C9 A:2TF701 2.9 34.6 1.0 C8 A:2TF701 3.0 37.1 1.0 O A:GLU32 3.0 33.8 1.0 CE1 A:HIS504 3.2 39.5 1.0 O4 A:2TF701 3.4 45.2 1.0 O3 A:2TF701 3.5 33.2 1.0 N A:SER34 3.8 38.9 1.0 O A:HOH818 4.0 28.4 1.0 O A:HOH857 4.1 41.0 1.0 ND1 A:HIS504 4.1 40.1 1.0 C A:GLU32 4.1 32.4 1.0 C10 A:2TF701 4.1 35.8 1.0 C A:LYS33 4.1 39.0 1.0 NE2 A:HIS504 4.1 45.0 1.0 C7 A:2TF701 4.3 36.9 1.0 CA A:LYS33 4.3 38.0 1.0 CB A:SER255 4.4 30.0 1.0 CB A:SER34 4.5 39.8 1.0 CA A:SER34 4.5 40.3 1.0 OG A:SER255 4.6 33.4 1.0 N A:LYS33 4.7 34.8 1.0 O A:LYS33 4.7 42.1 1.0 NH2 A:ARG525 4.9 42.3 1.0 CG1 A:VAL28 4.9 36.0 1.0

Fluorine binding site 3 out of 6 in the Human Gkrp Bound to Amg-0771 and Sorbitol-6-Phosphate


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-0771 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:38.1 occ:1.00 F1 A:2TF701 0.0 38.1 1.0 C21 A:2TF701 1.3 40.4 1.0 F2 A:2TF701 2.1 40.6 1.0 F3 A:2TF701 2.2 41.3 1.0 C12 A:2TF701 2.4 37.2 1.0 O4 A:2TF701 2.6 45.2 1.0 O3 A:2TF701 2.7 33.2 1.0 NH2 A:ARG525 2.9 42.3 1.0 C20 A:2TF701 3.0 37.1 1.0 NE A:ARG525 3.3 45.9 1.0 CZ A:ARG525 3.4 41.9 1.0 C9 A:2TF701 3.7 34.6 1.0 CE1 A:HIS504 3.8 39.5 1.0 NE2 A:HIS504 4.0 45.0 1.0 CB A:SER34 4.0 39.8 1.0 N A:SER34 4.3 38.9 1.0 C8 A:2TF701 4.5 37.1 1.0 CD A:ARG525 4.5 45.4 1.0 NH1 A:ARG525 4.6 45.3 1.0 C10 A:2TF701 4.6 35.8 1.0 CA A:SER34 4.7 40.3 1.0 CG A:ARG525 4.9 47.4 1.0 O A:GLU32 4.9 33.8 1.0 OE2 A:GLU25 5.0 65.1 1.0 ND1 A:HIS504 5.0 40.1 1.0

Fluorine binding site 4 out of 6 in the Human Gkrp Bound to Amg-0771 and Sorbitol-6-Phosphate


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-0771 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:36.3 occ:1.00 F2 B:2TF701 0.0 36.3 1.0 C21 B:2TF701 1.3 33.1 1.0 F1 B:2TF701 2.1 34.9 1.0 F3 B:2TF701 2.2 33.6 1.0 C12 B:2TF701 2.3 31.5 1.0 C9 B:2TF701 2.7 29.1 1.0 O3 B:2TF701 2.8 31.4 1.0 CG1 B:VAL28 3.2 31.7 1.0 C8 B:2TF701 3.4 31.3 1.0 C10 B:2TF701 3.4 30.7 1.0 C20 B:2TF701 3.6 32.5 1.0 NH2 B:ARG525 3.6 45.3 1.0 I B:IOD711 3.7 92.3 0.5 O B:GLU32 3.7 35.1 1.0 CA B:LYS33 3.9 34.2 1.0 O4 B:2TF701 4.0 39.5 1.0 CG2 B:VAL28 4.0 32.4 1.0 N B:SER34 4.0 34.9 1.0 CB B:VAL28 4.1 32.1 1.0 C B:LYS33 4.3 33.2 1.0 C B:GLU32 4.4 30.9 1.0 C7 B:2TF701 4.4 30.6 1.0 C11 B:2TF701 4.5 32.5 1.0 N B:LYS33 4.5 34.3 1.0 CZ B:ARG525 4.6 42.0 1.0 NE B:ARG525 4.8 39.0 1.0 OE2 B:GLU25 4.8 51.7 1.0 CB B:LYS33 4.8 35.7 1.0 C6 B:2TF701 4.9 31.4 1.0

Fluorine binding site 5 out of 6 in the Human Gkrp Bound to Amg-0771 and Sorbitol-6-Phosphate


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-0771 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:33.6 occ:1.00 F3 B:2TF701 0.0 33.6 1.0 C21 B:2TF701 1.3 33.1 1.0 F1 B:2TF701 2.1 34.9 1.0 F2 B:2TF701 2.2 36.3 1.0 C12 B:2TF701 2.4 31.5 1.0 C20 B:2TF701 2.8 32.5 1.0 C9 B:2TF701 3.1 29.1 1.0 CE1 B:HIS504 3.1 36.3 1.0 C8 B:2TF701 3.1 31.3 1.0 O4 B:2TF701 3.2 39.5 1.0 O B:GLU32 3.3 35.1 1.0 O3 B:2TF701 3.6 31.4 1.0 N B:SER34 3.7 34.9 1.0 NE2 B:HIS504 3.9 41.3 1.0 O B:HOH914 4.0 34.7 1.0 O B:HOH847 4.0 38.3 1.0 ND1 B:HIS504 4.0 39.2 1.0 C B:LYS33 4.1 33.2 1.0 C10 B:2TF701 4.3 30.7 1.0 C7 B:2TF701 4.4 30.6 1.0 CA B:LYS33 4.4 34.2 1.0 C B:GLU32 4.4 30.9 1.0 CB B:SER255 4.4 32.1 1.0 CB B:SER34 4.5 37.2 1.0 CA B:SER34 4.5 34.8 1.0 OG B:SER255 4.7 38.9 1.0 O B:LYS33 4.8 35.3 1.0 I B:IOD711 4.8 92.3 0.5 NH2 B:ARG525 4.9 45.3 1.0 N B:LYS33 4.9 34.3 1.0

Fluorine binding site 6 out of 6 in the Human Gkrp Bound to Amg-0771 and Sorbitol-6-Phosphate


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-0771 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:34.9 occ:1.00 F1 B:2TF701 0.0 34.9 1.0 C21 B:2TF701 1.3 33.1 1.0 F3 B:2TF701 2.1 33.6 1.0 F2 B:2TF701 2.1 36.3 1.0 C12 B:2TF701 2.4 31.5 1.0 O4 B:2TF701 2.5 39.5 1.0 O3 B:2TF701 2.7 31.4 1.0 C20 B:2TF701 2.9 32.5 1.0 NH2 B:ARG525 3.0 45.3 1.0 NE B:ARG525 3.2 39.0 1.0 CZ B:ARG525 3.4 42.0 1.0 C9 B:2TF701 3.7 29.1 1.0 I B:IOD711 3.8 92.3 0.5 CE1 B:HIS504 3.9 36.3 1.0 NE2 B:HIS504 4.1 41.3 1.0 N B:SER34 4.2 34.9 1.0 CB B:SER34 4.2 37.2 1.0 CD B:ARG525 4.4 39.1 1.0 C8 B:2TF701 4.4 31.3 1.0 NH1 B:ARG525 4.6 44.2 1.0 C10 B:2TF701 4.6 30.7 1.0 CA B:SER34 4.8 34.8 1.0 CG B:ARG525 4.9 37.5 1.0 C B:LYS33 5.0 33.2 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