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Chlorine 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:

Fluorine (F) 12 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Human Galactokinase 1 Bound with 2-(4-Chlorophenyl)-N- (Pyrimidin-2-Yl)Acetamide, PDB code: 6zh0:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6zh0

Go back to Chlorine Binding Sites List in 6zh0
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl403

b:79.8
occ:0.48
 CL1 A:WNP403 0.0 79.8 0.5
C12 A:WNP403 1.7 80.1 0.5
C14 A:WNP403 2.7 78.0 0.5
C11 A:WNP403 2.7 82.6 0.5
CB A:PHE303 2.9 78.4 1.0
CA A:PHE303 3.6 79.0 1.0
O A:ASP299 3.6 83.2 1.0
CD2 A:LEU355 3.8 75.7 1.0
C08 A:WNP403 4.0 78.6 0.5
C10 A:WNP403 4.0 83.0 0.5
N A:PHE303 4.1 82.1 1.0
CD1 A:LEU295 4.2 69.3 1.0
CA A:TYR300 4.2 84.2 1.0
C A:ASP299 4.3 85.3 1.0
C09 A:WNP403 4.5 81.2 0.5
N A:TYR300 4.5 85.6 1.0
CA A:LEU295 4.6 73.1 1.0
O A:TYR300 4.6 84.0 1.0
C A:TYR300 4.6 85.6 1.0
O06 A:WNP403 4.7 73.2 0.5
CB A:LEU295 4.7 69.8 1.0
O A:ALA291 4.8 69.7 1.0
N A:LEU295 4.8 74.6 1.0
C A:PHE303 5.0 79.3 1.0

Chlorine binding site 2 out of 4 in 6zh0

Go back to Chlorine Binding Sites List in 6zh0
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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
B:Cl403

b:54.5
occ:0.50
 CL1 B:WNP403 0.0 54.5 0.5
C12 B:WNP403 1.7 53.2 0.5
C14 B:WNP403 2.7 53.5 0.5
C11 B:WNP403 2.7 52.5 0.5
CG2 B:VAL220 3.9 51.0 1.0
C08 B:WNP403 4.0 53.1 0.5
C10 B:WNP403 4.0 51.9 0.5
CD1 B:LEU213 4.0 51.4 1.0
CA B:ALA219 4.1 57.0 1.0
CD2 B:LEU218 4.2 59.8 1.0
C B:ALA219 4.2 55.1 1.0
O B:LEU218 4.2 59.9 1.0
CD1 B:LEU355 4.4 46.7 1.0
CB B:LEU213 4.4 52.7 1.0
N B:ALA219 4.4 58.3 1.0
C09 B:WNP403 4.5 52.2 0.5
O B:ALA219 4.5 55.4 1.0
C B:LEU218 4.5 59.5 1.0
CG B:GLN382 4.6 53.6 1.0
N B:VAL220 4.6 53.6 1.0
CG B:LEU218 4.8 59.5 1.0
CG B:LEU213 4.8 51.7 1.0
O06 B:WNP403 4.9 55.5 0.5

Chlorine binding site 3 out of 4 in 6zh0

Go back to Chlorine Binding Sites List in 6zh0
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl 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
E:Cl403

b:49.8
occ:0.46
 CL1 E:WNP403 0.0 49.8 0.5
C12 E:WNP403 1.7 49.1 0.5
C14 E:WNP403 2.7 50.5 0.5
C11 E:WNP403 2.7 49.4 0.5
O E:LEU213 3.2 62.5 1.0
C10 E:WNP403 4.0 49.8 0.5
C08 E:WNP403 4.0 51.6 0.5
CG2 E:VAL220 4.1 45.5 1.0
C E:LEU213 4.1 61.8 1.0
C09 E:WNP403 4.5 50.3 0.5
CB E:LEU213 4.6 56.6 1.0
CB E:LEU218 4.6 58.9 1.0
CD1 E:LEU355 4.8 48.4 1.0
CA E:LEU213 4.8 58.9 1.0
N E:ALA219 4.8 55.6 1.0
C E:LEU218 4.8 58.1 1.0
C E:ALA219 4.9 51.3 1.0
CA E:ALA219 4.9 54.0 1.0
O E:LEU218 5.0 58.9 1.0
O06 E:WNP403 5.0 59.2 0.5

Chlorine binding site 4 out of 4 in 6zh0

Go back to Chlorine Binding Sites List in 6zh0
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl 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
D:Cl401

b:43.1
occ:0.46
 CL1 D:WNP401 0.0 43.1 0.5
C12 D:WNP401 1.7 41.5 0.5
C14 D:WNP401 2.7 41.2 0.5
C11 D:WNP401 2.7 41.8 0.5
CD2 D:LEU213 3.6 46.1 1.0
C10 D:WNP401 4.0 40.9 0.5
C08 D:WNP401 4.0 41.0 0.5
CA D:ALA219 4.1 54.8 1.0
CG2 D:VAL220 4.3 49.2 1.0
C D:ALA219 4.3 53.6 1.0
N D:ALA219 4.4 55.9 1.0
CD1 D:LEU355 4.5 44.2 1.0
O D:LEU218 4.5 57.9 1.0
C09 D:WNP401 4.5 40.8 0.5
N D:VAL220 4.5 52.6 1.0
C D:LEU218 4.5 57.3 1.0
CG D:LEU213 4.5 46.0 1.0
CE D:MET55 4.6 43.7 1.0
SD D:MET55 4.6 42.9 1.0
O D:ALA219 4.7 53.0 1.0
CA D:GLN382 4.8 46.5 1.0
CB D:LEU213 4.9 46.9 1.0
CB D:LEU218 4.9 56.6 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: Mon Jul 29 18:04:22 2024

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