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Fluorine in PDB 6zh0: 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: 6zh0 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) 118.77 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.529, 115.004, 120.849, 90, 100.65, 90
R / Rfree (%) 23.9 / 29

Other elements in 6zh0:

The structure of Structure of Human Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

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 6zh0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 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: 6zh0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 6zh0

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Fluorine binding site 1 out of 12 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
A:F403

b:70.1
occ:0.48
 F01 A:WNP403 0.0 70.1 0.5
C02 A:WNP403 1.3 72.9 0.5
F04 A:WNP403 2.1 73.9 0.5
F03 A:WNP403 2.1 73.7 0.5
C05 A:WNP403 2.4 74.4 0.5
O06 A:WNP403 2.7 73.2 0.5
CD2 A:LEU213 3.1 63.9 1.0
CG A:LEU213 3.2 66.3 1.0
N07 A:WNP403 3.5 76.8 0.5
CG1 A:VAL220 3.7 68.5 1.0
CB A:LEU213 4.0 66.9 1.0
CD1 A:LEU213 4.4 66.5 1.0
SD A:MET55 4.5 56.0 1.0
CD1 A:LEU40 4.6 57.7 1.0
C08 A:WNP403 4.7 78.6 0.5
O A:HOH519 4.9 58.8 1.0

Fluorine binding site 2 out of 12 in 6zh0

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Fluorine binding site 2 out of 12 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
A:F403

b:73.7
occ:0.48
 F03 A:WNP403 0.0 73.7 0.5
C02 A:WNP403 1.3 72.9 0.5
F04 A:WNP403 2.1 73.9 0.5
F01 A:WNP403 2.1 70.1 0.5
C05 A:WNP403 2.4 74.4 0.5
N07 A:WNP403 2.6 76.8 0.5
O A:HOH519 2.8 58.8 1.0
O06 A:WNP403 3.4 73.2 0.5
CG A:LEU213 3.5 66.3 1.0
CB A:LEU213 3.6 66.9 1.0
C08 A:WNP403 4.0 78.6 0.5
O A:LEU213 4.0 71.8 1.0
CD2 A:LEU213 4.1 63.9 1.0
O A:LEU218 4.2 81.8 1.0
CA A:LEU213 4.2 69.0 1.0
CB A:LEU218 4.3 84.2 1.0
O A:ASP215 4.5 82.2 1.0
C A:LEU213 4.5 71.5 1.0
C A:LEU218 4.6 82.6 1.0
CD1 A:LEU213 4.6 66.5 1.0
C09 A:WNP403 4.8 81.2 0.5
C14 A:WNP403 4.9 78.0 0.5

Fluorine binding site 3 out of 12 in 6zh0

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Fluorine binding site 3 out of 12 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
A:F403

b:73.9
occ:0.48
 F04 A:WNP403 0.0 73.9 0.5
C02 A:WNP403 1.3 72.9 0.5
F01 A:WNP403 2.1 70.1 0.5
F03 A:WNP403 2.1 73.7 0.5
C05 A:WNP403 2.4 74.4 0.5
O06 A:WNP403 3.0 73.2 0.5
N07 A:WNP403 3.2 76.8 0.5
CG1 A:VAL220 3.3 68.5 1.0
CD1 A:LEU355 3.7 75.9 1.0
C A:ALA219 3.7 76.2 1.0
O A:ALA219 3.7 77.2 1.0
CA A:ALA219 3.8 78.3 1.0
N A:ALA219 3.9 81.4 1.0
C A:LEU218 3.9 82.6 1.0
O A:LEU218 4.0 81.8 1.0
CB A:LEU218 4.1 84.2 1.0
N A:VAL220 4.2 73.4 1.0
CB A:VAL220 4.5 69.0 1.0
C08 A:WNP403 4.5 78.6 0.5
CA A:LEU218 4.6 85.6 1.0
O A:HOH519 4.7 58.8 1.0
CA A:VAL220 4.9 71.7 1.0
CG A:LEU213 5.0 66.3 1.0

Fluorine binding site 4 out of 12 in 6zh0

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Fluorine binding site 4 out of 12 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 4 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
B:F403

b:54.6
occ:0.50
 F01 B:WNP403 0.0 54.6 0.5
C02 B:WNP403 1.3 54.8 0.5
F03 B:WNP403 2.1 54.7 0.5
F04 B:WNP403 2.2 55.8 0.5
C05 B:WNP403 2.4 54.5 0.5
O06 B:WNP403 3.0 55.5 0.5
N07 B:WNP403 3.1 53.7 0.5
CA B:GLY298 3.1 56.8 1.0
O B:LEU295 3.2 48.8 1.0
C B:GLY298 3.6 57.6 1.0
CA B:LEU295 3.7 46.2 1.0
O B:ALA294 3.7 46.7 1.0
N B:ASP299 3.7 56.5 1.0
N B:GLY298 3.8 56.2 1.0
C B:LEU295 3.9 47.9 1.0
CD1 B:LEU295 4.0 44.8 1.0
O B:GLY298 4.4 59.8 1.0
C B:ALA294 4.5 45.8 1.0
C08 B:WNP403 4.5 53.1 0.5
N B:LEU295 4.5 45.5 1.0
N B:TYR300 4.6 54.3 1.0
C B:ASP299 4.6 54.9 1.0
CG B:LEU295 4.7 44.8 1.0
CB B:LEU295 4.8 45.4 1.0
CA B:ASP299 4.8 56.4 1.0
O B:ASP299 4.9 53.8 1.0
CA B:TYR300 5.0 53.1 1.0

Fluorine binding site 5 out of 12 in 6zh0

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Fluorine binding site 5 out of 12 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 5 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
B:F403

b:54.7
occ:0.50
 F03 B:WNP403 0.0 54.7 0.5
C02 B:WNP403 1.3 54.8 0.5
F01 B:WNP403 2.1 54.6 0.5
F04 B:WNP403 2.1 55.8 0.5
C05 B:WNP403 2.3 54.5 0.5
N07 B:WNP403 2.5 53.7 0.5
CA B:TYR300 3.3 53.1 1.0
N B:TYR300 3.4 54.3 1.0
O06 B:WNP403 3.4 55.5 0.5
C B:ASP299 3.5 54.9 1.0
O B:ASP299 3.6 53.8 1.0
C08 B:WNP403 3.8 53.1 0.5
CB B:TYR300 3.9 54.6 1.0
CB B:PHE303 3.9 42.5 1.0
N B:ASP299 4.0 56.5 1.0
CD1 B:LEU295 4.0 44.8 1.0
O B:ALA294 4.2 46.7 1.0
C B:GLY298 4.3 57.6 1.0
CG B:PHE303 4.4 41.4 1.0
CA B:ASP299 4.4 56.4 1.0
C09 B:WNP403 4.5 52.2 0.5
CA B:GLY298 4.5 56.8 1.0
C B:TYR300 4.5 51.4 1.0
CD2 B:LEU355 4.5 45.9 1.0
CA B:LEU295 4.6 46.2 1.0
CD2 B:PHE303 4.6 41.0 1.0
O B:TYR300 4.7 49.7 1.0
C B:ALA294 4.7 45.8 1.0
C14 B:WNP403 4.8 53.5 0.5
N B:LEU295 4.9 45.5 1.0
O B:GLY298 4.9 59.8 1.0
O B:LEU295 5.0 48.8 1.0
CD1 B:LEU218 5.0 59.2 1.0

Fluorine binding site 6 out of 12 in 6zh0

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Fluorine binding site 6 out of 12 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 6 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
B:F403

b:55.8
occ:0.50
 F04 B:WNP403 0.0 55.8 0.5
C02 B:WNP403 1.3 54.8 0.5
F03 B:WNP403 2.1 54.7 0.5
F01 B:WNP403 2.2 54.6 0.5
C05 B:WNP403 2.4 54.5 0.5
O06 B:WNP403 2.7 55.5 0.5
N B:TYR300 3.4 54.3 1.0
N07 B:WNP403 3.4 53.7 0.5
CB B:TYR300 3.4 54.6 1.0
C B:GLY298 3.6 57.6 1.0
CA B:TYR300 3.6 53.1 1.0
CA B:GLY298 3.7 56.8 1.0
CD1 B:LEU218 3.7 59.2 1.0
CD2 B:TYR300 3.8 58.1 1.0
O B:GLY298 3.8 59.8 1.0
N B:ASP299 3.9 56.5 1.0
C B:ASP299 4.1 54.9 1.0
CG B:TYR300 4.1 56.8 1.0
CA B:ASP299 4.6 56.4 1.0
C08 B:WNP403 4.7 53.1 0.5
O B:ASP299 4.7 53.8 1.0
N B:GLY298 4.9 56.2 1.0
CG B:LEU218 4.9 59.5 1.0
CE2 B:TYR300 4.9 59.9 1.0

Fluorine binding site 7 out of 12 in 6zh0

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Fluorine binding site 7 out of 12 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 7 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
E:F403

b:58.4
occ:0.46
 F01 E:WNP403 0.0 58.4 0.5
C02 E:WNP403 1.3 59.0 0.5
F03 E:WNP403 2.1 61.1 0.5
F04 E:WNP403 2.1 59.1 0.5
C05 E:WNP403 2.4 57.6 0.5
O06 E:WNP403 2.7 59.2 0.5
O E:LEU295 2.8 55.0 1.0
CA E:GLY298 3.1 53.7 1.0
N07 E:WNP403 3.4 54.1 0.5
CA E:LEU295 3.4 51.2 1.0
C E:LEU295 3.5 52.8 1.0
CD1 E:LEU295 3.6 51.5 1.0
C E:GLY298 3.6 53.2 1.0
N E:GLY298 3.8 53.5 1.0
CG E:LEU295 4.0 51.1 1.0
O E:GLY298 4.0 54.2 1.0
N E:ASP299 4.2 51.7 1.0
O E:ALA294 4.2 51.3 1.0
CB E:LEU295 4.3 50.6 1.0
N E:LEU295 4.5 50.0 1.0
N E:TYR300 4.6 49.6 1.0
C08 E:WNP403 4.6 51.6 0.5
C E:ALA294 4.8 49.7 1.0
N E:ARG296 4.8 52.6 1.0
C E:ASP299 4.8 49.4 1.0

Fluorine binding site 8 out of 12 in 6zh0

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Fluorine binding site 8 out of 12 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 8 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
E:F403

b:61.1
occ:0.46
 F03 E:WNP403 0.0 61.1 0.5
C02 E:WNP403 1.3 59.0 0.5
F01 E:WNP403 2.1 58.4 0.5
F04 E:WNP403 2.1 59.1 0.5
C05 E:WNP403 2.4 57.6 0.5
N07 E:WNP403 2.6 54.1 0.5
N E:TYR300 3.2 49.6 1.0
CA E:TYR300 3.3 48.6 1.0
CD1 E:LEU295 3.4 51.5 1.0
O06 E:WNP403 3.4 59.2 0.5
C E:ASP299 3.5 49.4 1.0
O E:ASP299 3.7 47.8 1.0
CA E:LEU295 3.7 51.2 1.0
C08 E:WNP403 3.9 51.6 0.5
C E:GLY298 3.9 53.2 1.0
CB E:TYR300 4.0 50.0 1.0
N E:ASP299 4.0 51.7 1.0
CB E:PHE303 4.1 43.2 1.0
O E:GLY298 4.2 54.2 1.0
O E:ALA294 4.2 51.3 1.0
CA E:GLY298 4.2 53.7 1.0
N E:LEU295 4.3 50.0 1.0
O E:LEU295 4.4 55.0 1.0
CG E:LEU295 4.4 51.1 1.0
CA E:ASP299 4.4 51.0 1.0
C E:ALA294 4.5 49.7 1.0
C09 E:WNP403 4.5 50.3 0.5
CB E:LEU295 4.6 50.6 1.0
C E:LEU295 4.6 52.8 1.0
CG E:PHE303 4.6 42.1 1.0
C E:TYR300 4.6 48.2 1.0
CD2 E:PHE303 4.7 41.7 1.0
N E:GLY298 4.9 53.5 1.0
C14 E:WNP403 5.0 50.5 0.5
O E:TYR300 5.0 46.9 1.0

Fluorine binding site 9 out of 12 in 6zh0

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Fluorine binding site 9 out of 12 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 9 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
E:F403

b:59.1
occ:0.46
 F04 E:WNP403 0.0 59.1 0.5
C02 E:WNP403 1.3 59.0 0.5
F03 E:WNP403 2.1 61.1 0.5
F01 E:WNP403 2.1 58.4 0.5
C05 E:WNP403 2.4 57.6 0.5
O E:GLY298 2.9 54.2 1.0
O06 E:WNP403 2.9 59.2 0.5
C E:GLY298 3.2 53.2 1.0
N E:TYR300 3.2 49.6 1.0
N07 E:WNP403 3.2 54.1 0.5
CB E:TYR300 3.4 50.0 1.0
CA E:GLY298 3.5 53.7 1.0
CA E:TYR300 3.5 48.6 1.0
CD1 E:LEU218 3.8 60.9 1.0
N E:ASP299 3.9 51.7 1.0
C E:ASP299 4.0 49.4 1.0
CA E:ASP299 4.5 51.0 1.0
C08 E:WNP403 4.6 51.6 0.5
N E:GLY298 4.6 53.5 1.0
CD2 E:LEU218 4.7 60.4 1.0
O E:LEU295 4.8 55.0 1.0
O E:ASP299 4.8 47.8 1.0
CG E:LEU218 4.9 60.9 1.0
CD1 E:LEU295 4.9 51.5 1.0

Fluorine binding site 10 out of 12 in 6zh0

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Fluorine binding site 10 out of 12 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 10 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:39.6
occ:0.46
 F01 D:WNP401 0.0 39.6 0.5
C02 D:WNP401 1.3 39.8 0.5
F03 D:WNP401 2.1 38.8 0.5
F04 D:WNP401 2.1 40.9 0.5
C05 D:WNP401 2.3 41.0 0.5
N07 D:WNP401 2.5 41.9 0.5
CA D:TYR300 2.7 48.2 1.0
N D:TYR300 2.9 48.5 1.0
CB D:TYR300 3.1 49.7 1.0
O06 D:WNP401 3.4 43.1 0.5
C D:ASP299 3.6 48.3 1.0
C08 D:WNP401 3.9 41.0 0.5
O D:ASP299 4.0 47.6 1.0
C D:TYR300 4.1 47.9 1.0
N D:ASP299 4.1 48.0 1.0
C D:GLY298 4.2 48.0 1.0
CD2 D:LEU218 4.3 56.2 1.0
CB D:PHE303 4.3 40.0 1.0
O D:GLY298 4.3 49.3 1.0
CD1 D:LEU295 4.4 37.5 1.0
O D:TYR300 4.5 47.5 1.0
CA D:ASP299 4.5 48.9 1.0
C09 D:WNP401 4.5 40.8 0.5
CD2 D:LEU355 4.8 43.5 1.0
CA D:GLY298 4.8 47.0 1.0
C14 D:WNP401 4.9 41.2 0.5
CG D:PHE303 4.9 39.0 1.0

Reference:

S.R.Mackinnon, T.Krojer, W.R.Foster, L.Diaz-Saez, M.Tang, K.V.M.Huber, F.Von Delft, K.Lai, P.E.Brennan, G.Arruda Bezerra, W.W.Yue. Fragment Screening Reveals Starting Points For Rational Design of Galactokinase 1 Inhibitors to Treat Classic Galactosemia. Acs Chem.Biol. V. 16 586 2021.
ISSN: ESSN 1554-8937
PubMed: 33724769
DOI: 10.1021/ACSCHEMBIO.0C00498
Page generated: Wed Apr 5 00:00:03 2023

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