Fluorine in PDB 7s4c: Crystal Structure of Inhibitor-Bound Galactokinase

All present enzymatic activity of Crystal Structure of Inhibitor-Bound Galactokinase:
2.7.1.6;

The structure of Crystal Structure of Inhibitor-Bound Galactokinase, PDB code: 7s4c was solved by F.G.Whitby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.61 / 2.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	129.216, 129.216, 240.789, 90, 90, 120
R / Rfree (%)	17.6 / 21.5

The structure of Crystal Structure of Inhibitor-Bound Galactokinase also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Inhibitor-Bound Galactokinase (pdb code 7s4c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Inhibitor-Bound Galactokinase, PDB code: 7s4c:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Inhibitor-Bound Galactokinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Inhibitor-Bound Galactokinase within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:31.3 occ:1.00 F1 A:V3V402 0.0 31.3 1.0 C1 A:V3V402 1.4 30.3 1.0 C2 A:V3V402 2.3 30.0 1.0 C25 A:V3V402 2.4 31.0 1.0 HB2 A:SER131 2.5 26.6 1.0 H5 A:V3V402 2.6 29.4 1.0 H18 A:V3V402 2.6 31.3 1.0 HB A:VAL129 3.0 30.7 1.0 CB A:SER131 3.3 27.3 1.0 HB3 A:SER131 3.4 27.7 1.0 HG23 A:THR61 3.4 25.7 1.0 HG21 A:THR61 3.4 25.5 1.0 HG1 A:THR77 3.6 29.0 1.0 C3 A:V3V402 3.6 30.4 1.0 O A:VAL130 3.6 25.9 1.0 C24 A:V3V402 3.7 31.4 1.0 HD13 A:LEU145 3.7 27.1 1.0 C A:VAL130 3.8 26.5 1.0 HG21 A:VAL129 3.8 31.5 1.0 CG2 A:THR61 3.8 25.4 1.0 CB A:VAL129 3.9 30.7 1.0 HG23 A:VAL129 3.9 32.1 1.0 HB3 A:SER79 3.9 50.0 1.0 N A:SER131 4.0 27.9 1.0 HB2 A:SER79 4.0 50.1 1.0 OG1 A:THR77 4.1 29.8 1.0 CG2 A:VAL129 4.1 31.6 1.0 N A:VAL130 4.1 26.0 1.0 C A:VAL129 4.1 27.0 1.0 HA A:VAL130 4.1 27.6 1.0 C4 A:V3V402 4.1 31.5 1.0 OG1 A:THR61 4.2 26.3 1.0 HD22 A:LEU145 4.2 27.8 1.0 OG A:SER131 4.2 26.2 1.0 CA A:SER131 4.2 27.2 1.0 O A:VAL129 4.3 26.6 1.0 HG1 A:THR61 4.3 26.0 1.0 CA A:VAL130 4.3 27.3 1.0 H A:VAL130 4.4 25.8 1.0 HG A:SER131 4.4 25.9 1.0 CB A:SER79 4.4 49.5 1.0 HB2 A:LEU145 4.5 27.2 1.0 H A:SER131 4.5 28.5 1.0 H17 A:V3V402 4.5 32.4 1.0 CD1 A:LEU145 4.6 27.3 1.0 HD21 A:LEU135 4.6 43.3 1.0 HG22 A:THR61 4.6 25.0 1.0 CA A:VAL129 4.6 27.3 1.0 HA A:SER131 4.6 27.0 1.0 CB A:THR61 4.7 25.4 1.0 HD11 A:LEU145 4.7 27.4 1.0 HG11 A:VAL129 4.8 32.7 1.0 HA A:THR61 4.8 26.0 1.0 O1 A:V3V402 4.8 30.2 1.0 CG1 A:VAL129 4.8 34.2 1.0 HG A:SER79 4.9 53.7 1.0 HB A:THR77 4.9 28.6 1.0 HG12 A:VAL129 4.9 32.5 1.0 H A:SER79 5.0 42.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Inhibitor-Bound Galactokinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Inhibitor-Bound Galactokinase within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:89.6 occ:1.00 F1 A:V3V403 0.0 89.6 1.0 C1 A:V3V403 1.4 80.4 1.0 HA A:LEU295 2.2 37.7 1.0 C25 A:V3V403 2.4 73.9 1.0 C2 A:V3V403 2.5 75.5 1.0 H18 A:V3V403 2.6 74.0 1.0 H5 A:V3V403 2.7 77.7 1.0 HD12 A:LEU295 2.9 38.5 1.0 CA A:LEU295 3.1 37.3 1.0 HD13 A:LEU295 3.2 37.0 1.0 HA A:TYR300 3.3 40.8 1.0 HB2 A:PHE303 3.4 33.0 1.0 HB2 A:LEU295 3.4 35.7 1.0 CD1 A:LEU295 3.4 37.5 1.0 HD2 A:PHE303 3.6 31.0 1.0 C24 A:V3V403 3.7 73.6 1.0 CB A:LEU295 3.7 36.2 1.0 C3 A:V3V403 3.7 74.5 1.0 N A:LEU295 3.7 35.9 1.0 HB3 A:TYR300 3.8 43.0 1.0 CD2 A:PHE303 3.9 30.4 1.0 O A:ALA294 3.9 37.6 1.0 HB3 A:PHE303 3.9 33.0 1.0 CB A:PHE303 4.0 32.5 1.0 CA A:TYR300 4.0 41.9 1.0 O A:LEU295 4.0 41.3 1.0 N A:TYR300 4.1 41.7 1.0 C A:ALA294 4.1 37.5 1.0 HA2 A:GLY298 4.1 44.2 1.0 C A:LEU295 4.1 40.1 1.0 CG A:PHE303 4.1 31.1 1.0 C4 A:V3V403 4.1 72.7 1.0 CG A:LEU295 4.2 36.9 1.0 C A:ASP299 4.2 41.6 1.0 O A:ASP299 4.2 39.3 1.0 HD11 A:LEU295 4.3 37.9 1.0 H A:ASP299 4.3 42.5 1.0 H A:LEU295 4.3 35.5 1.0 N A:ASP299 4.4 43.5 1.0 CB A:TYR300 4.4 43.4 1.0 HD21 A:LEU355 4.5 33.5 1.0 H A:TYR300 4.5 43.2 1.0 H17 A:V3V403 4.5 72.4 1.0 C A:GLY298 4.6 44.0 1.0 HB3 A:LEU295 4.6 36.0 1.0 H A:GLY298 4.7 44.1 1.0 CE2 A:PHE303 4.7 29.4 1.0 CA A:GLY298 4.7 44.9 1.0 HB3 A:ALA294 4.8 36.2 1.0 HG A:LEU295 4.8 37.2 1.0 HD22 A:LEU295 4.9 34.8 1.0 HD2 A:TYR300 4.9 46.8 1.0 HD22 A:LEU355 4.9 32.0 1.0 HB2 A:TYR300 4.9 43.0 1.0 CA A:ASP299 5.0 42.5 1.0 HE2 A:PHE303 5.0 29.4 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Inhibitor-Bound Galactokinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Inhibitor-Bound Galactokinase within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:39.5 occ:1.00 F1 B:V3V402 0.0 39.5 1.0 C1 B:V3V402 1.4 38.8 1.0 C2 B:V3V402 2.4 37.5 1.0 C25 B:V3V402 2.4 39.6 1.0 HB2 B:SER131 2.5 41.0 1.0 H5 B:V3V402 2.6 37.0 1.0 HG13 B:VAL129 2.6 37.6 1.0 H18 B:V3V402 2.6 40.8 1.0 HB B:VAL129 3.0 39.8 1.0 CG1 B:VAL129 3.3 38.5 1.0 HG11 B:VAL129 3.3 39.2 1.0 HG23 B:THR61 3.3 37.3 1.0 HG21 B:THR61 3.4 35.0 1.0 CB B:SER131 3.4 42.5 1.0 HD13 B:LEU145 3.4 32.4 1.0 HB3 B:SER131 3.5 43.3 1.0 HG1 B:THR77 3.5 47.0 1.0 C3 B:V3V402 3.6 37.1 1.0 CB B:VAL129 3.6 38.6 1.0 C B:VAL130 3.7 44.2 1.0 C24 B:V3V402 3.7 39.2 1.0 O B:VAL130 3.7 42.3 1.0 CG2 B:THR61 3.8 35.9 1.0 HA B:VAL130 3.9 46.5 1.0 N B:SER131 3.9 45.3 1.0 OG1 B:THR77 4.0 47.8 1.0 HB2 B:SER79 4.0 61.6 1.0 C B:VAL129 4.1 42.8 1.0 N B:VAL130 4.1 44.0 1.0 O B:VAL129 4.1 43.8 1.0 C4 B:V3V402 4.2 38.2 1.0 CA B:VAL130 4.2 45.9 1.0 HG12 B:VAL129 4.2 37.0 1.0 OG1 B:THR61 4.2 35.8 1.0 HB3 B:SER79 4.2 60.9 1.0 CA B:SER131 4.2 44.4 1.0 HG B:SER131 4.3 40.2 1.0 CD1 B:LEU145 4.3 31.4 1.0 OG B:SER131 4.3 41.0 1.0 H B:SER131 4.4 47.2 1.0 HD22 B:LEU145 4.4 32.3 1.0 HD11 B:LEU145 4.4 31.8 1.0 HG21 B:VAL129 4.5 36.3 1.0 HB2 B:LEU145 4.5 31.3 1.0 H B:VAL130 4.6 43.0 1.0 HG22 B:THR61 4.6 35.1 1.0 CA B:VAL129 4.6 40.7 1.0 H17 B:V3V402 4.6 40.3 1.0 CB B:THR61 4.6 36.2 1.0 HA B:SER131 4.6 43.6 1.0 CB B:SER79 4.6 62.2 1.0 CG2 B:VAL129 4.6 37.7 1.0 HA B:THR61 4.8 40.2 1.0 HD11 B:LEU135 4.8 59.2 1.0 HG1 B:THR61 4.8 35.1 1.0 O1 B:V3V402 4.9 35.6 1.0 HD12 B:LEU145 4.9 30.6 1.0 HA B:VAL129 4.9 40.1 1.0 HG B:SER79 5.0 62.1 1.0 HB B:THR77 5.0 46.0 1.0 HG23 B:VAL129 5.0 38.5 1.0

L.Liu, M.Tang, R.Pragani, F.G.Whitby, Y.Q.Zhang, B.Balakrishnan, Y.Fang, S.Karavadhi, D.Tao, C.A.Leclair, M.D.Hall, J.J.Marugan, M.Boxer, M.Shen, C.P.Hill, K.Lai, S.Patnaik. Structure-Based Optimization of Small Molecule Human Galactokinase Inhibitors Journal of Medicinal 2021CHEMISTRY.
DOI: 10.1021/ACS.JMEDCHEM.1C00945