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Sodium in PDB 4tw9: Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation

Enzymatic activity of Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation

All present enzymatic activity of Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation:
2.7.11.1; 2.7.11.26;

Protein crystallography data

The structure of Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation, PDB code: 4tw9 was solved by J.Richter, J.Bischof, M.Zaja, H.Kohlhof, O.Othersen, D.Vitt, V.Alscher, I.Pospiech, B.Garcia-Reyes, S.Berg, J.Leban, U.Knippschild, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.86 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.049, 135.707, 57.183, 90.00, 99.42, 90.00
R / Rfree (%) 20.6 / 29.8

Other elements in 4tw9:

The structure of Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation also contains other interesting chemical elements:

Fluorine (F) 10 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation (pdb code 4tw9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation, PDB code: 4tw9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4tw9

Go back to Sodium Binding Sites List in 4tw9
Sodium binding site 1 out of 4 in the Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1008

b:47.7
occ:1.00
 O A:LEU106 3.0 30.1 1.0
C A:PHE273 3.4 34.6 1.0
N A:ARG274 3.4 37.0 1.0
CB A:PHE273 3.4 31.3 1.0
O A:PHE273 3.6 33.7 1.0
C A:LEU106 3.7 30.6 1.0
CA A:ARG274 3.7 39.2 1.0
CB A:LEU106 3.8 34.4 1.0
OD1 A:ASP110 3.8 40.4 1.0
CB A:ASP110 3.9 29.9 1.0
CA A:PHE273 4.0 33.5 1.0
CG A:ARG274 4.0 41.4 1.0
CA A:LEU106 4.1 32.3 1.0
CG A:ASP110 4.2 35.2 1.0
CD1 A:PHE277 4.2 37.9 1.0
CB A:PHE277 4.3 41.7 1.0
CB A:ARG274 4.4 40.7 1.0
N A:ASP110 4.5 26.7 1.0
CA A:ASP110 4.6 28.1 1.0
CG A:PHE277 4.6 40.6 1.0
CG A:PHE273 4.7 30.3 1.0
N A:LEU107 4.7 31.0 1.0
CG A:LEU106 4.8 34.1 1.0
CD2 A:LEU106 4.8 34.7 1.0
O A:ARG270 4.9 35.8 1.0
CE1 A:TYR284 4.9 42.7 1.0

Sodium binding site 2 out of 4 in 4tw9

Go back to Sodium Binding Sites List in 4tw9
Sodium binding site 2 out of 4 in the Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1009

b:50.8
occ:1.00
 O A:HOH1146 3.3 20.6 1.0
O A:HOH1133 3.5 23.6 1.0
NZ A:LYS38 3.5 24.5 1.0
CD1 A:ILE23 3.6 40.5 1.0
CE A:LYS38 3.9 31.8 1.0
CB A:ASP149 3.9 38.8 1.0
OD2 A:ASP149 4.0 41.3 1.0
O5 A:3861010 4.0 56.9 1.0
CA A:GLY18 4.0 43.8 1.0
CG A:ASP149 4.1 39.2 1.0
CA A:ASP149 4.1 40.0 1.0
CD A:LYS38 4.3 28.6 1.0
CG1 A:ILE23 4.3 32.7 1.0
N A:ASP149 4.3 37.2 1.0
CD1 A:ILE148 4.5 20.7 1.0
N A:GLY18 4.5 44.4 1.0
OE2 A:GLU52 4.7 45.3 1.0
F4 A:3861010 4.7 60.4 1.0
OD1 A:ASP149 4.8 43.0 1.0
C19 A:3861010 4.8 58.2 1.0
F5 A:3861010 4.9 69.0 1.0
O A:PHE20 4.9 42.2 0.5
O A:PHE20 4.9 42.9 0.5

Sodium binding site 3 out of 4 in 4tw9

Go back to Sodium Binding Sites List in 4tw9
Sodium binding site 3 out of 4 in the Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1005

b:47.7
occ:1.00
 O B:HOH1124 2.9 24.6 1.0
O B:LEU106 3.1 30.1 1.0
CB B:PHE273 3.4 30.3 1.0
OD1 B:ASP110 3.6 28.8 1.0
C B:PHE273 3.6 29.4 1.0
N B:ARG274 3.7 30.0 1.0
C B:LEU106 3.7 29.9 1.0
CB B:ASP110 3.8 29.6 1.0
CB B:LEU106 3.9 30.1 1.0
O B:PHE273 3.9 26.7 1.0
CG B:ASP110 4.0 32.2 1.0
CA B:ARG274 4.0 31.8 1.0
CA B:LEU106 4.1 30.1 1.0
CA B:PHE273 4.1 30.0 1.0
CG B:ARG274 4.2 33.9 1.0
N B:ASP110 4.3 25.9 1.0
CA B:ASP110 4.4 27.5 1.0
CD1 B:PHE277 4.5 29.2 1.0
N B:LEU107 4.5 29.9 1.0
O B:ARG270 4.5 29.9 1.0
CB B:PHE277 4.6 31.4 1.0
CG B:PHE273 4.6 29.3 1.0
CE1 B:TYR284 4.6 46.5 1.0
CD2 B:LEU106 4.7 31.1 1.0
CB B:ARG274 4.8 32.8 1.0
CG B:LEU106 4.8 31.3 1.0
CG B:PHE277 4.9 30.1 1.0
OD2 B:ASP110 5.0 36.1 1.0

Sodium binding site 4 out of 4 in 4tw9

Go back to Sodium Binding Sites List in 4tw9
Sodium binding site 4 out of 4 in the Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1DELTA and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1006

b:44.1
occ:1.00
 O B:HOH1180 3.1 13.8 1.0
O B:HOH1184 3.1 13.4 1.0
NZ B:LYS38 3.3 25.8 1.0
O B:HOH1230 3.3 21.0 1.0
O B:HOH1193 3.4 17.4 1.0
CD1 B:ILE23 3.5 37.5 1.0
O5 B:3861007 3.8 50.1 1.0
CA B:GLY18 3.9 36.8 1.0
CE B:LYS38 3.9 28.8 1.0
N B:GLY18 4.1 36.5 1.0
CB B:ASP149 4.1 36.9 1.0
CG B:ASP149 4.2 39.2 1.0
CD B:LYS38 4.2 29.2 1.0
CG1 B:ILE23 4.3 33.4 1.0
CA B:ASP149 4.3 36.1 1.0
OD2 B:ASP149 4.4 37.0 1.0
CD1 B:ILE148 4.5 30.6 1.0
OD1 B:ASP149 4.6 38.1 1.0
OE2 B:GLU52 4.7 35.4 1.0
N B:ASP149 4.7 34.5 1.0
C16 B:3861007 4.7 43.1 1.0
C18 B:3861007 4.8 44.3 1.0
C19 B:3861007 4.9 56.7 1.0
O B:HOH1175 4.9 20.9 1.0
C B:GLY18 4.9 38.8 1.0
F5 B:3861007 4.9 68.1 1.0
O B:PHE20 5.0 35.6 1.0
N B:SER19 5.0 38.0 1.0

Reference:

J.Richter, J.Bischof, M.Zaja, H.Kohlhof, O.Othersen, D.Vitt, V.Alscher, I.Pospiech, B.Garcia-Reyes, S.Berg, J.Leban, U.Knippschild. Difluoro-Dioxolo-Benzoimidazol-Benzamides As Potent Inhibitors of CK1 Delta and Epsilon with Nanomolar Inhibitory Activity on Cancer Cell Proliferation. J.Med.Chem. V. 57 7933 2014.
ISSN: ISSN 0022-2623
PubMed: 25191940
DOI: 10.1021/JM500600B
Page generated: Tue Dec 15 07:39:03 2020

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