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

Enzymatic activity of 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;

Protein crystallography data

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

Resolution Low / High (Å) 38.26 / 2.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.190, 86.160, 137.970, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening (pdb code 5wbr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening, PDB code: 5wbr:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5wbr

Go back to Fluorine Binding Sites List in 5wbr
Fluorine binding site 1 out of 6 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:93.6
occ:1.00
 F1 A:A3Y301 0.0 93.6 1.0
C19 A:A3Y301 1.3 95.4 1.0
F2 A:A3Y301 2.1 95.4 1.0
F3 A:A3Y301 2.1 93.6 1.0
C2 A:A3Y301 2.4 99.8 1.0
H1 A:A3Y301 2.5 0.7 1.0
C1 A:A3Y301 2.9 0.6 1.0
CG2 A:VAL250 3.4 58.2 1.0
C3 A:A3Y301 3.7 0.3 1.0
CG1 A:VAL250 3.7 58.4 1.0
CD A:PRO247 3.8 57.7 1.0
C18 A:A3Y301 4.2 0.7 1.0
CB A:PRO246 4.2 62.3 1.0
CB A:VAL250 4.2 58.9 1.0
H8 A:A3Y301 4.2 0.1 1.0
C5 A:A3Y301 4.3 0.5 1.0
CA A:PRO246 4.3 60.8 1.0
CB A:CYS289 4.3 56.5 1.0
SG A:CYS289 4.5 60.4 1.0
N5 A:A3Y301 4.8 0.6 1.0
CG A:PRO247 4.8 62.1 1.0
N A:PRO247 4.9 57.3 1.0
C4 A:A3Y301 4.9 0.9 1.0

Fluorine binding site 2 out of 6 in 5wbr

Go back to Fluorine Binding Sites List in 5wbr
Fluorine binding site 2 out of 6 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:95.4
occ:1.00
 F2 A:A3Y301 0.0 95.4 1.0
C19 A:A3Y301 1.3 95.4 1.0
F1 A:A3Y301 2.1 93.6 1.0
F3 A:A3Y301 2.1 93.6 1.0
C2 A:A3Y301 2.4 99.8 1.0
H1 A:A3Y301 3.0 0.7 1.0
C1 A:A3Y301 3.1 0.6 1.0
C3 A:A3Y301 3.3 0.3 1.0
CA A:GLU227 3.5 75.5 1.0
C18 A:A3Y301 3.7 0.7 1.0
CB A:GLU227 3.8 77.1 1.0
N A:GLU227 3.9 75.9 1.0
CB A:PRO246 4.0 62.3 1.0
N5 A:A3Y301 4.3 0.6 1.0
CA A:PRO246 4.4 60.8 1.0
C5 A:A3Y301 4.4 0.5 1.0
C A:ALA226 4.4 78.9 1.0
C4 A:A3Y301 4.5 0.9 1.0
O A:ALA226 4.5 78.7 1.0
CB A:ALA244 4.6 57.9 1.0
C A:GLU227 4.6 77.7 1.0
OE2 A:GLU227 4.7 84.7 1.0
H22 A:A3Y301 4.8 0.9 1.0
O A:GLU227 4.8 78.5 1.0
CG A:PRO246 4.8 66.3 1.0
CD A:PRO246 4.9 62.5 1.0
N A:PRO246 4.9 60.9 1.0
N1 A:A3Y301 4.9 0.1 1.0

Fluorine binding site 3 out of 6 in 5wbr

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Fluorine binding site 3 out of 6 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:93.6
occ:1.00
 F3 A:A3Y301 0.0 93.6 1.0
C19 A:A3Y301 1.3 95.4 1.0
F1 A:A3Y301 2.1 93.6 1.0
F2 A:A3Y301 2.1 95.4 1.0
C2 A:A3Y301 2.5 99.8 1.0
C18 A:A3Y301 2.7 0.7 1.0
N5 A:A3Y301 2.9 0.6 1.0
C3 A:A3Y301 3.0 0.3 1.0
C1 A:A3Y301 3.7 0.6 1.0
CA A:PRO246 3.7 60.8 1.0
H1 A:A3Y301 3.9 0.7 1.0
CD A:PRO247 4.0 57.7 1.0
SG A:CYS289 4.1 60.4 1.0
O A:HOH403 4.1 54.3 1.0
CB A:PRO246 4.2 62.3 1.0
CA A:GLY286 4.2 56.6 1.0
CB A:CYS289 4.3 56.5 1.0
N A:PRO246 4.3 60.9 1.0
C4 A:A3Y301 4.4 0.9 1.0
O A:PHE245 4.7 62.4 1.0
C A:PHE245 4.7 62.8 1.0
H22 A:A3Y301 4.7 0.9 1.0
C A:PRO246 4.8 62.6 1.0
N A:PRO247 4.8 57.3 1.0
CD A:PRO246 4.9 62.5 1.0
CB A:ALA244 4.9 57.9 1.0
O A:GLY286 4.9 57.9 1.0
C5 A:A3Y301 4.9 0.5 1.0

Fluorine binding site 4 out of 6 in 5wbr

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Fluorine binding site 4 out of 6 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 4 of Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:76.2
occ:1.00
 F1 B:A3Y301 0.0 76.2 1.0
C19 B:A3Y301 1.3 73.5 1.0
F2 B:A3Y301 2.1 72.3 1.0
F3 B:A3Y301 2.2 75.3 1.0
C2 B:A3Y301 2.4 70.7 1.0
H1 B:A3Y301 2.5 66.5 1.0
C1 B:A3Y301 2.7 67.0 1.0
OE1 B:GLU227 3.3 0.5 1.0
C3 B:A3Y301 3.7 70.3 1.0
CG2 B:VAL250 4.1 69.8 1.0
CD B:GLU227 4.2 0.1 1.0
C5 B:A3Y301 4.2 68.1 1.0
CB B:GLU227 4.2 61.6 1.0
C18 B:A3Y301 4.2 67.8 1.0
H3 B:A3Y301 4.3 76.2 1.0
CA B:GLU227 4.5 60.2 1.0
N B:GLU227 4.7 60.6 1.0
CG B:GLU227 4.8 74.6 1.0
C4 B:A3Y301 4.8 68.0 1.0
CB B:PRO246 4.9 60.9 1.0
N5 B:A3Y301 4.9 67.9 1.0
N1 B:A3Y301 4.9 67.1 1.0
OE2 B:GLU227 5.0 86.7 1.0

Fluorine binding site 5 out of 6 in 5wbr

Go back to Fluorine Binding Sites List in 5wbr
Fluorine binding site 5 out of 6 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 5 of Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:72.3
occ:1.00
 F2 B:A3Y301 0.0 72.3 1.0
C19 B:A3Y301 1.3 73.5 1.0
F1 B:A3Y301 2.1 76.2 1.0
F3 B:A3Y301 2.1 75.3 1.0
C2 B:A3Y301 2.5 70.7 1.0
C18 B:A3Y301 2.9 67.8 1.0
C3 B:A3Y301 3.0 70.3 1.0
N5 B:A3Y301 3.3 67.9 1.0
CB B:PRO246 3.5 60.9 1.0
C1 B:A3Y301 3.6 67.0 1.0
CA B:GLU227 3.8 60.2 1.0
H1 B:A3Y301 3.9 66.5 1.0
CB B:GLU227 4.0 61.6 1.0
CA B:PRO246 4.1 59.6 1.0
N B:GLU227 4.3 60.6 1.0
C4 B:A3Y301 4.3 68.0 1.0
H16 B:A3Y301 4.5 67.3 1.0
CG B:PRO246 4.6 64.0 1.0
OE1 B:GLU227 4.6 0.5 1.0
CB B:ALA244 4.6 56.2 1.0
N B:PRO246 4.7 59.3 1.0
CD B:PRO246 4.8 59.8 1.0
C5 B:A3Y301 4.8 68.1 1.0
CD B:PRO247 4.8 63.7 1.0
C B:ALA226 4.8 65.7 1.0
C B:GLU227 4.9 64.5 1.0
O B:ALA226 5.0 66.4 1.0
O B:GLU227 5.0 63.6 1.0
N1 B:A3Y301 5.0 67.1 1.0

Fluorine binding site 6 out of 6 in 5wbr

Go back to Fluorine Binding Sites List in 5wbr
Fluorine binding site 6 out of 6 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 6 of Structure of Human Ketohexokinase Complexed with Hits From Fragment Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:75.3
occ:1.00
 F3 B:A3Y301 0.0 75.3 1.0
C19 B:A3Y301 1.4 73.5 1.0
F2 B:A3Y301 2.1 72.3 1.0
F1 B:A3Y301 2.2 76.2 1.0
C2 B:A3Y301 2.4 70.7 1.0
C18 B:A3Y301 3.1 67.8 1.0
C3 B:A3Y301 3.2 70.3 1.0
CG2 B:VAL250 3.3 69.8 1.0
CD B:PRO247 3.3 63.7 1.0
C1 B:A3Y301 3.4 67.0 1.0
N5 B:A3Y301 3.5 67.9 1.0
H1 B:A3Y301 3.5 66.5 1.0
CB B:PRO246 4.0 60.9 1.0
CB B:CYS289 4.1 62.9 1.0
CA B:PRO246 4.1 59.6 1.0
CG B:PRO247 4.3 68.2 1.0
SG B:CYS289 4.4 66.8 1.0
N B:PRO247 4.5 62.9 1.0
C4 B:A3Y301 4.5 68.0 1.0
CB B:VAL250 4.6 70.2 1.0
C5 B:A3Y301 4.7 68.1 1.0
CG1 B:VAL250 4.8 69.9 1.0
C B:PRO246 4.9 66.1 1.0

Reference:

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
Page generated: Thu Aug 1 16:30:50 2024

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