Fluorine in PDB 6zgz: Structure of Human Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide

Enzymatic activity of Structure of Human Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide

All present enzymatic activity of Structure of Human Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide:
2.7.1.6;

Protein crystallography data

The structure of Structure of Human Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide, PDB code: 6zgz was solved by S.R.Mackinnon, G.A.Bezerra, M.Zhang, W.Foster, T.Krojer, J.Brandao-Neto, A.Douangamath, C.Arrowsmith, A.Edwards, C.Bountra, P.Brennan, K.Lai, W.W.Yue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.49 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.210, 114.299, 120.807, 90.00, 100.54, 90.00
R / Rfree (%) 21.4 / 25.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide (pdb code 6zgz). 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 Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide, PDB code: 6zgz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6zgz

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Fluorine binding site 1 out of 3 in the Structure of Human Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide


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 Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:50.4
occ:0.60
 F D:SSY401 0.0 50.4 0.6
C9 D:SSY401 1.3 49.7 0.6
F2 D:SSY401 2.1 49.6 0.6
F1 D:SSY401 2.2 52.0 0.6
O D:LEU213 2.3 48.6 1.0
C8 D:SSY401 2.5 47.4 0.6
O1 D:SSY401 2.9 47.5 0.6
O D:HOH598 3.4 47.0 1.0
C D:LEU213 3.5 46.2 1.0
N D:SSY401 3.5 46.0 0.6
CA D:GLY196 3.8 34.5 1.0
O D:HOH523 3.9 44.8 1.0
CB D:LEU213 4.2 41.8 1.0
O D:SER214 4.3 62.0 1.0
O D:GLY196 4.3 32.4 1.0
C D:SER214 4.3 55.5 1.0
N D:SER214 4.4 48.5 1.0
CA D:LEU213 4.4 42.6 1.0
C D:GLY196 4.5 32.6 1.0
CA D:SER214 4.6 52.7 1.0
N D:ASP215 4.7 53.8 1.0
C6 D:SSY401 4.8 44.0 0.6
O D:ASP215 4.9 51.9 1.0
C D:ASP215 4.9 53.3 1.0
N D:LEU213 5.0 42.0 1.0

Fluorine binding site 2 out of 3 in 6zgz

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Fluorine binding site 2 out of 3 in the Structure of Human Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide


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 Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:52.0
occ:0.60
 F1 D:SSY401 0.0 52.0 0.6
C9 D:SSY401 1.4 49.7 0.6
F D:SSY401 2.2 50.4 0.6
F2 D:SSY401 2.2 49.6 0.6
C8 D:SSY401 2.6 47.4 0.6
O1 D:SSY401 3.2 47.5 0.6
CA D:PRO216 3.3 55.4 1.0
N D:SSY401 3.6 46.0 0.6
CB D:PRO216 3.7 58.5 1.0
N D:PRO216 3.9 55.0 1.0
O D:ASP215 4.0 51.9 1.0
O D:HOH598 4.0 47.0 1.0
C D:ASP215 4.1 53.3 1.0
O D:LEU213 4.1 48.6 1.0
OE1 D:GLN382 4.2 56.3 1.0
CD D:GLN382 4.4 53.0 1.0
NE2 D:GLN382 4.4 54.2 1.0
C D:PRO216 4.4 56.1 1.0
O D:SER214 4.6 62.0 1.0
O D:PRO216 4.6 56.9 1.0
CD D:PRO216 4.8 56.6 1.0
CG D:PRO216 4.9 58.6 1.0
C D:SER214 4.9 55.5 1.0
C6 D:SSY401 4.9 44.0 0.6
N D:ASP215 5.0 53.8 1.0

Fluorine binding site 3 out of 3 in 6zgz

Go back to Fluorine Binding Sites List in 6zgz
Fluorine binding site 3 out of 3 in the Structure of Human Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide


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 Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:49.6
occ:0.60
 F2 D:SSY401 0.0 49.6 0.6
C9 D:SSY401 1.3 49.7 0.6
F D:SSY401 2.1 50.4 0.6
F1 D:SSY401 2.2 52.0 0.6
C8 D:SSY401 2.4 47.4 0.6
N D:SSY401 2.6 46.0 0.6
O D:LEU213 2.7 48.6 1.0
O D:ASP215 2.8 51.9 1.0
C D:ASP215 3.0 53.3 1.0
N D:ASP215 3.0 53.8 1.0
C D:SER214 3.1 55.5 1.0
C D:LEU213 3.3 46.2 1.0
O D:SER214 3.4 62.0 1.0
N D:PRO216 3.4 55.0 1.0
O1 D:SSY401 3.5 47.5 0.6
CA D:ASP215 3.6 53.6 1.0
CA D:PRO216 3.7 55.4 1.0
N D:SER214 3.8 48.5 1.0
CA D:SER214 3.9 52.7 1.0
C6 D:SSY401 4.0 44.0 0.6
CB D:LEU213 4.3 41.8 1.0
CA D:LEU213 4.4 42.6 1.0
CD D:PRO216 4.5 56.6 1.0
CB D:PRO216 4.6 58.5 1.0
C7 D:SSY401 4.6 42.4 0.6
CB D:ASP215 4.7 53.8 1.0
C D:PRO216 4.8 56.1 1.0

Reference:

S.R.Mackinnon, T.Krojer, W.R.Foster, M.Tang, F.Von Delft, K.Lai, P.Brennan, G.A.Bezerra, W.W.Yue. Fragment Screening Reveals Starting Points For Rational Design of Galactokinase 1 Inhibitors to Treat Classic Galactosemia To Be Published.
Page generated: Sun Dec 13 13:46:07 2020

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