Fluorine in PDB 5wbp: Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening

All present enzymatic activity of Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening:
2.7.1.3;

The structure of Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening, PDB code: 5wbp was solved by J.Pandit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.17 / 2.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.910, 85.020, 138.780, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.9

The binding sites of Fluorine atom in the Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening (pdb code 5wbp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening, PDB code: 5wbp:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:0.0 occ:1.00 F1 A:A2J301 0.0 0.0 1.0 C9 A:A2J301 1.3 0.9 1.0 F2 A:A2J301 2.1 0.4 1.0 F3 A:A2J301 2.1 1.0 1.0 C8 A:A2J301 2.4 0.8 1.0 N2 A:A2J301 2.6 0.9 1.0 O A:HOH401 3.2 64.8 1.0 CA A:PRO246 3.3 59.7 1.0 N A:PRO246 3.5 59.8 1.0 C7 A:A2J301 3.7 0.9 1.0 C A:PHE245 3.9 63.8 1.0 CA A:GLY286 3.9 59.5 1.0 CB A:PRO246 3.9 60.2 1.0 O A:PHE245 4.0 63.8 1.0 C4 A:A2J301 4.0 0.3 1.0 CD A:PRO246 4.1 60.1 1.0 CB A:ALA244 4.1 60.5 1.0 CD A:PRO247 4.2 63.4 1.0 O1 A:A2J301 4.2 0.2 1.0 N A:PHE245 4.4 60.5 1.0 C A:PRO246 4.6 64.8 1.0 N A:GLY286 4.6 60.9 1.0 H4 A:A2J301 4.6 0.9 1.0 CG A:PRO246 4.7 63.9 1.0 N1 A:A2J301 4.7 0.2 1.0 N A:PRO247 4.8 61.9 1.0 CA A:PHE245 4.8 59.0 1.0 C3 A:A2J301 4.8 0.0 1.0 SG A:CYS289 4.9 71.8 1.0 C5 A:A2J301 4.9 0.2 1.0 CB A:CYS289 5.0 67.7 1.0

Fluorine binding site 2 out of 3 in the Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:0.4 occ:1.00 F2 A:A2J301 0.0 0.4 1.0 C9 A:A2J301 1.3 0.9 1.0 F1 A:A2J301 2.1 0.0 1.0 F3 A:A2J301 2.1 1.0 1.0 C8 A:A2J301 2.4 0.8 1.0 O1 A:A2J301 2.9 0.2 1.0 C7 A:A2J301 2.9 0.9 1.0 N2 A:A2J301 3.4 0.9 1.0 CD A:PRO247 3.7 63.4 1.0 CB A:CYS289 3.7 67.7 1.0 SG A:CYS289 3.8 71.8 1.0 CA A:PRO246 4.1 59.7 1.0 CG2 A:VAL250 4.2 74.6 1.0 N1 A:A2J301 4.2 0.2 1.0 CB A:PRO246 4.4 60.2 1.0 CG1 A:VAL250 4.4 74.7 1.0 C4 A:A2J301 4.6 0.3 1.0 CG A:PRO247 4.7 66.8 1.0 N A:PRO247 4.7 61.9 1.0 CA A:GLY286 4.9 59.5 1.0 H1 A:A2J301 4.9 1.0 1.0 CB A:VAL250 4.9 74.8 1.0 N A:PRO246 4.9 59.8 1.0 C5 A:A2J301 5.0 0.2 1.0 C A:PRO246 5.0 64.8 1.0

Fluorine binding site 3 out of 3 in the Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:1.0 occ:1.00 F3 A:A2J301 0.0 1.0 1.0 C9 A:A2J301 1.3 0.9 1.0 F2 A:A2J301 2.1 0.4 1.0 F1 A:A2J301 2.1 0.0 1.0 C8 A:A2J301 2.3 0.8 1.0 C7 A:A2J301 3.1 0.9 1.0 O1 A:A2J301 3.2 0.2 1.0 N2 A:A2J301 3.2 0.9 1.0 CA A:GLU227 3.6 89.4 1.0 CB A:GLU227 3.8 91.3 1.0 CB A:PRO246 4.0 60.2 1.0 N A:GLU227 4.0 90.0 1.0 CA A:PRO246 4.3 59.7 1.0 N1 A:A2J301 4.3 0.2 1.0 C A:ALA226 4.4 93.5 1.0 O A:ALA226 4.4 93.5 1.0 C4 A:A2J301 4.4 0.3 1.0 CB A:ALA244 4.4 60.5 1.0 N A:PRO246 4.7 59.8 1.0 CD A:PRO246 4.7 60.1 1.0 O A:HOH401 4.8 64.8 1.0 CG A:PRO246 4.8 63.9 1.0 C A:GLU227 4.8 90.3 1.0 C5 A:A2J301 4.9 0.2 1.0

K.Huard, K.Ahn, P.Amor, D.A.Beebe, K.A.Borzilleri, B.A.Chrunyk, S.B.Coffey, Y.Cong, E.L.Conn, J.S.Culp, M.S.Dowling, M.F.Gorgoglione, J.A.Gutierrez, J.D.Knafels, E.A.Lachapelle, J.Pandit, K.D.Parris, S.Perez, J.A.Pfefferkorn, D.A.Price, B.Raymer, T.T.Ross, A.Shavnya, A.C.Smith, T.A.Subashi, G.J.Tesz, B.A.Thuma, M.Tu, J.D.Weaver, Y.Weng, J.M.Withka, G.Xing, T.V.Magee. Discovery of Fragment-Derived Small Molecules For in Vivo Inhibition of Ketohexokinase (Khk). J. Med. Chem. V. 60 7835 2017.
ISSN: ISSN 1520-4804
PubMed: 28853885
DOI: 10.1021/ACS.JMEDCHEM.7B00947