Fluorine in PDB 8ug1: Crystal Structure of Khk-C and Compound 13

The structure of Crystal Structure of Khk-C and Compound 13, PDB code: 8ug1 was solved by J.D.Durbin, S.Y.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.90 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.583, 86.793, 136.432, 90, 90, 90
R / Rfree (%)	17.3 / 20.5

The binding sites of Fluorine atom in the Crystal Structure of Khk-C and Compound 13 (pdb code 8ug1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Khk-C and Compound 13, PDB code: 8ug1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Khk-C and Compound 13


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 Khk-C and Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:54.4 occ:1.00 F1 A:WNH301 0.0 54.4 1.0 C17 A:WNH301 1.4 61.4 1.0 F2 A:WNH301 2.1 60.8 1.0 F3 A:WNH301 2.1 59.5 1.0 C6 A:WNH301 2.4 57.6 1.0 C1 A:WNH301 2.8 47.9 1.0 CA A:PRO246 3.5 37.5 1.0 N3 A:WNH301 3.6 43.1 1.0 CD A:PRO247 3.6 38.8 1.0 CB A:PRO246 3.8 44.0 1.0 CG2 A:VAL250 3.8 45.3 1.0 CB A:CYS289 4.1 36.1 1.0 O A:HOH531 4.1 61.2 1.0 O A:HOH403 4.2 72.9 1.0 C5 A:WNH301 4.2 46.0 1.0 SG A:CYS289 4.2 47.6 1.0 N A:PRO246 4.4 39.9 1.0 N A:PRO247 4.6 36.9 1.0 C A:PRO246 4.6 38.0 1.0 C7 A:WNH301 4.7 44.6 1.0 CG A:PRO247 4.7 39.9 1.0 CA A:GLY286 4.8 36.8 1.0 CG1 A:VAL250 4.8 41.9 1.0 O A:HOH443 4.9 38.1 1.0 CG A:GLU227 4.9 64.7 1.0 CD A:PRO246 4.9 35.1 1.0 O A:PHE245 4.9 36.0 1.0 N2 A:WNH301 5.0 48.0 1.0 C A:PHE245 5.0 38.7 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Khk-C and Compound 13


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 Khk-C and Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:60.8 occ:1.00 F2 A:WNH301 0.0 60.8 1.0 C17 A:WNH301 1.3 61.4 1.0 F3 A:WNH301 2.0 59.5 1.0 F1 A:WNH301 2.1 54.4 1.0 C6 A:WNH301 2.3 57.6 1.0 N3 A:WNH301 3.0 43.1 1.0 C1 A:WNH301 3.1 47.9 1.0 CA A:GLU227 3.5 51.7 1.0 CB A:ALA244 3.5 36.9 1.0 CB A:PRO246 3.7 44.0 1.0 CA A:PRO246 3.9 37.5 1.0 O A:HOH471 4.0 60.9 1.0 CG A:GLU227 4.0 64.7 1.0 CB A:GLU227 4.1 55.5 1.0 CD A:PRO246 4.1 35.1 1.0 N A:PRO246 4.1 39.9 1.0 O A:HOH443 4.1 38.1 1.0 C7 A:WNH301 4.1 44.6 1.0 C5 A:WNH301 4.2 46.0 1.0 O A:GLU227 4.3 50.0 1.0 N A:GLU227 4.3 45.8 1.0 C A:GLU227 4.3 50.7 1.0 O A:HOH531 4.3 61.2 1.0 CG A:PRO246 4.4 43.4 1.0 O A:HOH528 4.5 52.5 1.0 O A:ALA226 4.6 50.1 1.0 N2 A:WNH301 4.7 48.0 1.0 C A:ALA226 4.7 54.1 1.0 CA A:ALA244 4.8 39.3 1.0 O A:HOH403 4.8 72.9 1.0 C A:PHE245 4.8 38.7 1.0 N A:PHE245 4.9 35.0 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Khk-C and Compound 13


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 Khk-C and Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:59.5 occ:1.00 F3 A:WNH301 0.0 59.5 1.0 C17 A:WNH301 1.3 61.4 1.0 F2 A:WNH301 2.0 60.8 1.0 F1 A:WNH301 2.1 54.4 1.0 C6 A:WNH301 2.3 57.6 1.0 N3 A:WNH301 2.7 43.1 1.0 O A:HOH443 2.8 38.1 1.0 CA A:PRO246 3.2 37.5 1.0 N A:PRO246 3.3 39.9 1.0 C A:PHE245 3.5 38.7 1.0 C1 A:WNH301 3.6 47.9 1.0 CA A:GLY286 3.6 36.8 1.0 O A:PHE245 3.6 36.0 1.0 CB A:PRO246 3.9 44.0 1.0 N A:PHE245 3.9 35.0 1.0 CD A:PRO246 3.9 35.1 1.0 CB A:ALA244 4.0 36.9 1.0 C7 A:WNH301 4.0 44.6 1.0 CD A:PRO247 4.2 38.8 1.0 CA A:PHE245 4.3 33.3 1.0 N A:GLY286 4.4 40.1 1.0 C A:PRO246 4.4 38.0 1.0 CG A:PRO246 4.6 43.4 1.0 C A:ALA244 4.6 38.1 1.0 C5 A:WNH301 4.7 46.0 1.0 CA A:ALA244 4.7 39.3 1.0 C A:GLY286 4.7 38.1 1.0 N A:PRO247 4.7 36.9 1.0 O A:GLY286 4.8 41.0 1.0 N2 A:WNH301 4.9 48.0 1.0 N6 A:WNH301 4.9 45.4 1.0 SG A:CYS289 4.9 47.6 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Khk-C and Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Khk-C and Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:56.8 occ:1.00 F1 B:WNH301 0.0 56.8 1.0 C17 B:WNH301 1.4 52.5 1.0 F3 B:WNH301 2.1 54.4 1.0 F2 B:WNH301 2.2 62.6 1.0 C6 B:WNH301 2.4 51.3 1.0 C1 B:WNH301 2.8 48.7 1.0 O B:HOH588 3.3 61.1 1.0 CA B:PRO246 3.5 41.2 1.0 N3 B:WNH301 3.5 46.8 1.0 CD B:PRO247 3.6 45.2 1.0 CB B:PRO246 3.7 43.4 1.0 O B:HOH406 3.8 64.1 1.0 C5 B:WNH301 4.2 46.8 1.0 CB B:CYS289 4.3 44.5 1.0 N B:PRO246 4.4 40.8 1.0 SG B:CYS289 4.4 49.8 1.0 CG2 B:VAL250 4.5 59.9 1.0 CG B:GLU227 4.5 52.9 1.0 N B:PRO247 4.5 45.1 1.0 C B:PRO246 4.6 45.6 1.0 C7 B:WNH301 4.6 42.9 1.0 O B:HOH590 4.7 52.9 1.0 CG B:PRO247 4.8 46.2 1.0 CA B:GLY286 4.9 41.7 1.0 CG B:PRO246 4.9 49.7 1.0 N2 B:WNH301 4.9 44.0 1.0 O B:PHE245 5.0 46.1 1.0 O B:HOH469 5.0 41.6 1.0 C B:PHE245 5.0 42.6 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Khk-C and Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Khk-C and Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:62.6 occ:1.00 F2 B:WNH301 0.0 62.6 1.0 C17 B:WNH301 1.3 52.5 1.0 F3 B:WNH301 2.0 54.4 1.0 F1 B:WNH301 2.2 56.8 1.0 C6 B:WNH301 2.3 51.3 1.0 N3 B:WNH301 3.0 46.8 1.0 C1 B:WNH301 3.1 48.7 1.0 CB B:ALA244 3.2 38.1 1.0 CA B:GLU227 3.4 43.6 1.0 O B:HOH507 3.6 44.9 1.0 CG B:GLU227 3.7 52.9 1.0 CB B:GLU227 3.8 49.5 1.0 CB B:PRO246 3.9 43.4 1.0 O B:HOH590 4.0 52.9 1.0 O B:HOH588 4.0 61.1 1.0 CA B:PRO246 4.0 41.2 1.0 C7 B:WNH301 4.1 42.9 1.0 O B:GLU227 4.1 48.4 1.0 N B:GLU227 4.2 43.5 1.0 O B:HOH469 4.2 41.6 1.0 C B:GLU227 4.2 42.7 1.0 N B:PRO246 4.3 40.8 1.0 C5 B:WNH301 4.3 46.8 1.0 CD B:PRO246 4.4 43.5 1.0 O B:ALA226 4.4 40.8 1.0 CG B:PRO246 4.5 49.7 1.0 CA B:ALA244 4.6 39.1 1.0 C B:ALA226 4.6 40.0 1.0 N2 B:WNH301 4.7 44.0 1.0 N B:PHE245 4.7 41.1 1.0 O B:HOH406 4.8 64.1 1.0 CD B:GLU227 4.8 63.8 1.0 C B:PHE245 4.9 42.6 1.0 C B:ALA244 4.9 47.0 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Khk-C and Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Khk-C and Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:54.4 occ:1.00 F3 B:WNH301 0.0 54.4 1.0 C17 B:WNH301 1.3 52.5 1.0 F2 B:WNH301 2.0 62.6 1.0 F1 B:WNH301 2.1 56.8 1.0 C6 B:WNH301 2.4 51.3 1.0 N3 B:WNH301 2.7 46.8 1.0 O B:HOH469 3.0 41.6 1.0 CA B:PRO246 3.1 41.2 1.0 N B:PRO246 3.2 40.8 1.0 C B:PHE245 3.4 42.6 1.0 O B:PHE245 3.5 46.1 1.0 C1 B:WNH301 3.6 48.7 1.0 CA B:GLY286 3.7 41.7 1.0 N B:PHE245 3.7 41.1 1.0 CB B:ALA244 3.7 38.1 1.0 CB B:PRO246 3.7 43.4 1.0 CD B:PRO246 4.0 43.5 1.0 C7 B:WNH301 4.1 42.9 1.0 CD B:PRO247 4.2 45.2 1.0 CA B:PHE245 4.2 42.5 1.0 C B:PRO246 4.3 45.6 1.0 C B:ALA244 4.4 47.0 1.0 CG B:PRO246 4.5 49.7 1.0 CA B:ALA244 4.5 39.1 1.0 N B:GLY286 4.6 40.7 1.0 N B:PRO247 4.7 45.1 1.0 C5 B:WNH301 4.7 46.8 1.0 C B:GLY286 4.7 42.3 1.0 O B:GLY286 4.8 45.3 1.0 O B:HOH588 4.9 61.1 1.0 N2 B:WNH301 4.9 44.0 1.0 N6 B:WNH301 5.0 42.4 1.0 O B:HOH507 5.0 44.9 1.0

T.B.Durham, J.Hao, P.Spinazze, D.R.Stack, J.L.Toth, S.Massey, C.T.Mbofana, R.D.Johnston, J.P.Lineswala, A.Wrobleski, J.M.Minguez, C.Perez, D.L.Smith, J.Lamar, R.Leon, C.Corkins, J.Durbin, F.Tung, S.Guo, R.J.Linder, N.Yumibe, W.Wang, J.Mackrell, M.Antonellis, B.Mascaro. Identification of LY3522348: A Highly Selective and Orally Efficacious Ketohexokinase Inhibitor. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37992274
DOI: 10.1021/ACS.JMEDCHEM.3C01410