Fluorine in PDB 4op2: Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate

The structure of Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate, PDB code: 4op2 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)	36.32 / 2.24
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	149.053, 149.053, 131.833, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 27

The structure of Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate also contains other interesting chemical elements:

Iodine

(I)

26 atoms

The binding sites of Fluorine atom in the Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate (pdb code 4op2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate, PDB code: 4op2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Gkrp Bound to Amg-0471 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 Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:58.4 occ:1.00 F2 A:2UX701 0.0 58.4 1.0 C20 A:2UX701 1.3 55.8 1.0 F1 A:2UX701 2.2 62.3 1.0 F3 A:2UX701 2.2 68.4 1.0 C13 A:2UX701 2.3 47.9 1.0 C14 A:2UX701 2.8 46.2 1.0 CE1 A:HIS504 2.8 43.8 1.0 C9 A:2UX701 2.9 40.3 1.0 C10 A:2UX701 3.0 39.8 1.0 ND1 A:HIS504 3.2 39.5 1.0 O1 A:2UX701 3.4 46.2 1.0 NE2 A:HIS504 3.5 45.4 1.0 CG A:MET522 3.7 34.6 1.0 CG A:HIS504 4.0 43.1 1.0 CD2 A:HIS504 4.2 44.8 1.0 C8 A:2UX701 4.2 37.6 1.0 C11 A:2UX701 4.3 37.4 1.0 CA A:MET522 4.5 37.2 1.0 CB A:MET522 4.7 36.9 1.0 SD A:MET522 4.8 33.0 1.0 O A:HOH817 4.8 27.8 1.0 N A:MET522 4.8 38.7 1.0 CB A:ARG525 4.8 43.4 1.0 CG A:ARG525 5.0 49.3 1.0 CB A:HIS504 5.0 41.6 1.0 O A:ALA521 5.0 32.9 1.0

Fluorine binding site 2 out of 6 in the Gkrp Bound to Amg-0471 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 Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:68.4 occ:1.00 F3 A:2UX701 0.0 68.4 1.0 C20 A:2UX701 1.3 55.8 1.0 F2 A:2UX701 2.2 58.4 1.0 F1 A:2UX701 2.2 62.3 1.0 C13 A:2UX701 2.3 47.9 1.0 O1 A:2UX701 2.6 46.2 1.0 C10 A:2UX701 2.9 39.8 1.0 O A:ALA521 2.9 32.9 1.0 O A:HOH801 3.0 36.9 1.0 C A:ALA521 3.2 38.6 1.0 C9 A:2UX701 3.3 40.3 1.0 CB A:ARG525 3.4 43.4 1.0 CA A:MET522 3.5 37.2 1.0 N A:MET522 3.5 38.7 1.0 C14 A:2UX701 3.7 46.2 1.0 C11 A:2UX701 3.8 37.4 1.0 CG A:MET522 3.9 34.6 1.0 CB A:ALA521 3.9 34.0 1.0 CG A:ARG525 4.1 49.3 1.0 CA A:ALA521 4.2 34.0 1.0 CB A:MET522 4.3 36.9 1.0 NE A:ARG525 4.4 59.9 1.0 C8 A:2UX701 4.5 37.6 1.0 C A:MET522 4.5 41.8 1.0 CA A:ARG525 4.6 46.4 1.0 N A:ARG525 4.7 43.2 1.0 O A:MET522 4.7 46.2 1.0 CE1 A:HIS504 4.8 43.8 1.0 C12 A:2UX701 4.8 36.1 1.0 CD A:ARG525 4.9 49.1 1.0

Fluorine binding site 3 out of 6 in the Gkrp Bound to Amg-0471 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 Gkrp Bound to Amg-0471 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:2UX701 0.0 62.3 1.0 C20 A:2UX701 1.3 55.8 1.0 F2 A:2UX701 2.2 58.4 1.0 F3 A:2UX701 2.2 68.4 1.0 C13 A:2UX701 2.3 47.9 1.0 O1 A:2UX701 2.5 46.2 1.0 C14 A:2UX701 2.8 46.2 1.0 NE A:ARG525 3.0 59.9 1.0 CG A:ARG525 3.1 49.3 1.0 CB A:ARG525 3.3 43.4 1.0 NE2 A:HIS504 3.4 45.4 1.0 CE1 A:HIS504 3.4 43.8 1.0 CD A:ARG525 3.6 49.1 1.0 C10 A:2UX701 3.7 39.8 1.0 CZ A:ARG525 4.0 56.0 1.0 O A:HOH801 4.2 36.9 1.0 NH2 A:ARG525 4.2 51.8 1.0 CD2 A:HIS504 4.3 44.8 1.0 ND1 A:HIS504 4.3 39.5 1.0 C9 A:2UX701 4.3 40.3 1.0 C11 A:2UX701 4.7 37.4 1.0 CG A:HIS504 4.8 43.1 1.0 O A:ALA521 4.8 32.9 1.0 CA A:ARG525 4.8 46.4 1.0

Fluorine binding site 4 out of 6 in the Gkrp Bound to Amg-0471 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 Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:60.2 occ:1.00 F2 B:2UX701 0.0 60.2 1.0 C20 B:2UX701 1.3 44.4 1.0 F1 B:2UX701 2.1 50.4 1.0 C13 B:2UX701 2.3 36.9 1.0 F3 B:2UX701 2.3 59.9 1.0 C14 B:2UX701 2.6 32.1 1.0 C9 B:2UX701 2.8 30.4 1.0 C10 B:2UX701 2.9 30.7 1.0 CE1 B:HIS504 2.9 35.6 1.0 O B:HOH843 3.1 33.9 1.0 ND1 B:HIS504 3.2 36.3 1.0 O1 B:2UX701 3.4 34.1 1.0 NE2 B:HIS504 3.6 40.2 1.0 CG B:MET522 4.0 31.3 1.0 CG B:HIS504 4.0 36.4 1.0 C8 B:2UX701 4.1 33.0 1.0 O B:HOH900 4.1 28.5 1.0 CD2 B:HIS504 4.2 36.3 1.0 C11 B:2UX701 4.3 31.8 1.0 O B:GLU32 4.6 35.4 1.0 CB B:SER255 4.9 34.6 1.0 CA B:MET522 4.9 32.6 1.0 SD B:MET522 5.0 28.1 1.0

Fluorine binding site 5 out of 6 in the Gkrp Bound to Amg-0471 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 Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:59.9 occ:1.00 F3 B:2UX701 0.0 59.9 1.0 C20 B:2UX701 1.3 44.4 1.0 F1 B:2UX701 2.1 50.4 1.0 F2 B:2UX701 2.3 60.2 1.0 C13 B:2UX701 2.3 36.9 1.0 O1 B:2UX701 2.6 34.1 1.0 C10 B:2UX701 2.8 30.7 1.0 O B:ALA521 3.0 34.8 1.0 O B:HOH801 3.1 28.0 1.0 C9 B:2UX701 3.2 30.4 1.0 C B:ALA521 3.2 36.0 1.0 N B:MET522 3.4 34.1 1.0 CA B:MET522 3.5 32.6 1.0 C14 B:2UX701 3.7 32.1 1.0 CB B:ARG525 3.7 38.5 1.0 C11 B:2UX701 3.7 31.8 1.0 CG B:MET522 3.8 31.3 1.0 CB B:ALA521 3.9 33.5 1.0 CA B:ALA521 4.2 32.5 1.0 CB B:MET522 4.2 32.8 1.0 C8 B:2UX701 4.3 33.0 1.0 CG B:ARG525 4.4 37.9 1.0 NE B:ARG525 4.6 47.7 1.0 C B:MET522 4.6 31.6 1.0 C12 B:2UX701 4.7 33.1 1.0 N B:ARG525 4.9 40.1 1.0 CE1 B:HIS504 4.9 35.6 1.0 O B:HOH843 4.9 33.9 1.0 CA B:ARG525 4.9 40.3 1.0 O B:MET522 4.9 36.3 1.0

Fluorine binding site 6 out of 6 in the Gkrp Bound to Amg-0471 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 Gkrp Bound to Amg-0471 and Sorbitol-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:50.4 occ:1.00 F1 B:2UX701 0.0 50.4 1.0 C20 B:2UX701 1.3 44.4 1.0 F3 B:2UX701 2.1 59.9 1.0 F2 B:2UX701 2.1 60.2 1.0 C13 B:2UX701 2.4 36.9 1.0 O1 B:2UX701 2.7 34.1 1.0 C14 B:2UX701 3.0 32.1 1.0 CG B:ARG525 3.2 37.9 1.0 NE2 B:HIS504 3.3 40.2 1.0 CB B:ARG525 3.3 38.5 1.0 CE1 B:HIS504 3.4 35.6 1.0 NE B:ARG525 3.5 47.7 1.0 C10 B:2UX701 3.7 30.7 1.0 O B:HOH803 3.8 42.5 1.0 CD B:ARG525 3.9 40.8 1.0 CD2 B:HIS504 4.0 36.3 1.0 ND1 B:HIS504 4.1 36.3 1.0 O B:HOH801 4.2 28.0 1.0 C9 B:2UX701 4.3 30.4 1.0 CG B:HIS504 4.5 36.4 1.0 CZ B:ARG525 4.5 52.0 1.0 O B:ALA521 4.7 34.8 1.0 NH2 B:ARG525 4.7 51.6 1.0 C11 B:2UX701 4.8 31.8 1.0 CA B:MET522 4.8 32.6 1.0 CG B:MET522 4.8 31.3 1.0 CA B:ARG525 4.9 40.3 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