Fluorine in PDB 4op3: Human Gkrp Bound to Amg-5112 and Sorbitol-6-Phosphate

The structure of Human Gkrp Bound to Amg-5112 and Sorbitol-6-Phosphate, PDB code: 4op3 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)	29.59 / 2.82
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	148.913, 148.913, 132.403, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 26.6

The structure of Human Gkrp Bound to Amg-5112 and Sorbitol-6-Phosphate also contains other interesting chemical elements:

Iodine

(I)

25 atoms

The binding sites of Fluorine atom in the Human Gkrp Bound to Amg-5112 and Sorbitol-6-Phosphate (pdb code 4op3). 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-5112 and Sorbitol-6-Phosphate, PDB code: 4op3:
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-5112 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-5112 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:66.1 occ:1.00 F2 A:2UY701 0.0 66.1 1.0 C24 A:2UY701 1.3 64.7 1.0 F3 A:2UY701 2.2 65.5 1.0 F1 A:2UY701 2.2 62.3 1.0 C11 A:2UY701 2.3 61.7 1.0 O1 A:2UY701 2.6 61.5 1.0 C1 A:2UY701 2.9 56.9 1.0 O A:ALA521 2.9 36.1 1.0 CB A:ARG525 3.1 50.0 1.0 C A:ALA521 3.2 31.5 1.0 CA A:MET522 3.3 33.2 1.0 N A:MET522 3.4 32.0 1.0 C2 A:2UY701 3.4 54.1 1.0 C23 A:2UY701 3.7 63.8 1.0 CG A:ARG525 3.7 56.6 1.0 C5 A:2UY701 3.8 50.2 1.0 CG A:MET522 3.9 31.6 1.0 CB A:ALA521 4.0 27.3 1.0 NE A:ARG525 4.2 66.6 1.0 CB A:MET522 4.2 32.6 1.0 CA A:ALA521 4.2 28.9 1.0 CA A:ARG525 4.3 45.3 1.0 C A:MET522 4.4 35.0 1.0 N A:ARG525 4.4 42.8 1.0 C3 A:2UY701 4.5 54.3 1.0 CD A:ARG525 4.5 61.9 1.0 O A:MET522 4.6 39.3 1.0 N1 A:2UY701 4.8 49.7 1.0 CE1 A:HIS504 4.8 31.7 1.0 OH A:TYR24 4.8 45.9 1.0

Fluorine binding site 2 out of 6 in the Human Gkrp Bound to Amg-5112 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-5112 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:65.5 occ:1.00 F3 A:2UY701 0.0 65.5 1.0 C24 A:2UY701 1.3 64.7 1.0 F2 A:2UY701 2.2 66.1 1.0 F1 A:2UY701 2.2 62.3 1.0 C11 A:2UY701 2.4 61.7 1.0 C2 A:2UY701 2.5 54.1 1.0 C1 A:2UY701 2.7 56.9 1.0 C23 A:2UY701 3.0 63.8 1.0 CE1 A:HIS504 3.2 31.7 1.0 ND1 A:HIS504 3.4 31.2 1.0 O1 A:2UY701 3.5 61.5 1.0 CG A:MET522 3.6 31.6 1.0 C3 A:2UY701 3.8 54.3 1.0 NE2 A:HIS504 4.0 32.3 1.0 C5 A:2UY701 4.1 50.2 1.0 CG A:HIS504 4.2 31.6 1.0 CA A:MET522 4.4 33.2 1.0 N A:MET522 4.5 32.0 1.0 CD2 A:HIS504 4.6 31.4 1.0 CB A:MET522 4.6 32.6 1.0 SD A:MET522 4.7 30.7 1.0 C A:ALA521 4.8 31.5 1.0 C4 A:2UY701 4.8 53.8 1.0 CB A:ARG525 4.8 50.0 1.0 O A:ALA521 4.9 36.1 1.0 CB A:ALA521 4.9 27.3 1.0 N1 A:2UY701 4.9 49.7 1.0 O A:GLU32 4.9 24.7 1.0 CG A:ARG525 5.0 56.6 1.0

Fluorine binding site 3 out of 6 in the Human Gkrp Bound to Amg-5112 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-5112 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:62.3 occ:1.00 F1 A:2UY701 0.0 62.3 1.0 C24 A:2UY701 1.4 64.7 1.0 F3 A:2UY701 2.2 65.5 1.0 F2 A:2UY701 2.2 66.1 1.0 C11 A:2UY701 2.4 61.7 1.0 C23 A:2UY701 2.8 63.8 1.0 O1 A:2UY701 2.9 61.5 1.0 CG A:ARG525 3.0 56.6 1.0 CE1 A:HIS504 3.0 31.7 1.0 NE2 A:HIS504 3.1 32.3 1.0 NE A:ARG525 3.2 66.6 1.0 O A:HOH818 3.3 26.3 1.0 CB A:ARG525 3.4 50.0 1.0 CD A:ARG525 3.6 61.9 1.0 C1 A:2UY701 3.7 56.9 1.0 ND1 A:HIS504 3.8 31.2 1.0 CD2 A:HIS504 4.0 31.4 1.0 C2 A:2UY701 4.2 54.1 1.0 CZ A:ARG525 4.3 64.7 1.0 CG A:HIS504 4.4 31.6 1.0 NH2 A:ARG525 4.6 60.6 1.0 C5 A:2UY701 4.8 50.2 1.0 CG A:MET522 4.9 31.6 1.0 CA A:ARG525 4.9 45.3 1.0

Fluorine binding site 4 out of 6 in the Human Gkrp Bound to Amg-5112 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-5112 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:48.2 occ:1.00 F2 B:2UY701 0.0 48.2 1.0 C24 B:2UY701 1.4 53.2 1.0 F1 B:2UY701 2.2 59.7 1.0 F3 B:2UY701 2.2 51.4 1.0 C11 B:2UY701 2.4 50.8 1.0 O1 B:2UY701 2.8 49.9 1.0 C23 B:2UY701 2.9 49.2 1.0 NE B:ARG525 3.0 53.0 1.0 CG B:ARG525 3.1 47.6 1.0 NE2 B:HIS504 3.1 25.1 1.0 CB B:ARG525 3.2 44.3 1.0 CE1 B:HIS504 3.4 25.6 1.0 CD B:ARG525 3.6 49.9 1.0 C1 B:2UY701 3.8 48.1 1.0 CD2 B:HIS504 3.9 24.5 1.0 CZ B:ARG525 4.0 57.2 1.0 ND1 B:HIS504 4.2 25.9 1.0 NH2 B:ARG525 4.2 58.2 1.0 C2 B:2UY701 4.4 47.3 1.0 CG B:HIS504 4.5 25.0 1.0 O B:ALA521 4.7 25.3 1.0 CA B:ARG525 4.7 40.9 1.0 C5 B:2UY701 4.8 46.4 1.0 CA B:MET522 5.0 28.3 1.0 CE2 B:PHE526 5.0 32.0 1.0 CG B:MET522 5.0 27.1 1.0

Fluorine binding site 5 out of 6 in the Human Gkrp Bound to Amg-5112 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-5112 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:51.4 occ:1.00 F3 B:2UY701 0.0 51.4 1.0 C24 B:2UY701 1.3 53.2 1.0 F1 B:2UY701 2.2 59.7 1.0 F2 B:2UY701 2.2 48.2 1.0 C11 B:2UY701 2.4 50.8 1.0 O1 B:2UY701 2.8 49.9 1.0 C1 B:2UY701 2.9 48.1 1.0 O B:ALA521 3.0 25.3 1.0 C B:ALA521 3.3 24.9 1.0 CA B:MET522 3.3 28.3 1.0 C2 B:2UY701 3.3 47.3 1.0 N B:MET522 3.4 26.9 1.0 CG B:MET522 3.4 27.1 1.0 CB B:ARG525 3.6 44.3 1.0 C23 B:2UY701 3.7 49.2 1.0 C5 B:2UY701 3.8 46.4 1.0 CB B:MET522 3.9 27.1 1.0 CB B:ALA521 4.1 22.6 1.0 CA B:ALA521 4.3 23.7 1.0 CG B:ARG525 4.4 47.6 1.0 C3 B:2UY701 4.4 47.0 1.0 NE B:ARG525 4.4 53.0 1.0 C B:MET522 4.5 30.5 1.0 CE1 B:HIS504 4.6 25.6 1.0 NE2 B:HIS504 4.7 25.1 1.0 N1 B:2UY701 4.8 48.0 1.0 N B:ARG525 4.8 40.3 1.0 CA B:ARG525 4.8 40.9 1.0 SD B:MET522 4.9 27.0 1.0 O B:MET522 4.9 34.0 1.0 ND1 B:HIS504 5.0 25.9 1.0

Fluorine binding site 6 out of 6 in the Human Gkrp Bound to Amg-5112 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-5112 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:59.7 occ:1.00 F1 B:2UY701 0.0 59.7 1.0 C24 B:2UY701 1.3 53.2 1.0 F3 B:2UY701 2.2 51.4 1.0 F2 B:2UY701 2.2 48.2 1.0 C11 B:2UY701 2.3 50.8 1.0 CE1 B:HIS504 2.7 25.6 1.0 C23 B:2UY701 2.8 49.2 1.0 C2 B:2UY701 2.9 47.3 1.0 C1 B:2UY701 3.0 48.1 1.0 ND1 B:HIS504 3.0 25.9 1.0 NE2 B:HIS504 3.2 25.1 1.0 O1 B:2UY701 3.6 49.9 1.0 CG B:HIS504 3.7 25.0 1.0 CD2 B:HIS504 3.9 24.5 1.0 CG B:MET522 4.0 27.1 1.0 C3 B:2UY701 4.2 47.0 1.0 C5 B:2UY701 4.3 46.4 1.0 SD B:MET522 4.7 27.0 1.0 CB B:HIS504 4.8 25.9 1.0 O B:GLU32 4.9 24.3 1.0 CA B:MET522 4.9 28.3 1.0 CB B:MET522 5.0 27.1 1.0

N.Tamayo, M.H.Norman, M.D.Bartberger, Y.Bo, J.Chen, S.Chmait, R.Cupples, C.Fotsch, C.Hale, F-T.Hong, S.R.Jordan, L.Liu, D.J.Lloyd, C.Moyer, N.Nishimura, G.Sivits, S.Tadesse, G.Van, K.C.Yang, D.J.St. Jean. Small Molecule Disruptors of the Glucokinase-Glucokinase Regulatory Protein Interaction: 5. New Aryl Sulfones Series, Optimization Through Conformational Analysis J.Med.Chem. 2014.
ISSN: ISSN 0022-2623