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Fluorine 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:

Chlorine (Cl) 2 atoms
Sodium (Na) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 10 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 4tw9

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Fluorine binding site 1 out of 10 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 Fluorine with other atoms in the F 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:F1010

b:69.0
occ:1.00
 F5 A:3861010 0.0 69.0 1.0
C19 A:3861010 1.4 58.2 1.0
O5 A:3861010 2.2 56.9 1.0
F4 A:3861010 2.3 60.4 1.0
O4 A:3861010 2.3 56.4 1.0
C16 A:3861010 3.0 47.5 1.0
C15 A:3861010 3.1 47.3 1.0
CG A:MET82 3.1 40.3 1.0
O A:HOH1146 3.6 20.6 1.0
CE A:MET80 3.6 36.5 1.0
CB A:MET82 3.9 37.2 1.0
CB A:LYS38 4.1 34.3 1.0
C18 A:3861010 4.2 43.9 1.0
CD A:LYS38 4.2 28.6 1.0
C17 A:3861010 4.3 42.8 1.0
SD A:MET82 4.4 43.9 1.0
CG A:LYS38 4.6 29.8 1.0
CG1 A:ILE23 4.6 32.7 1.0
OH A:TYR56 4.8 20.5 1.0
CE A:MET82 4.8 38.4 1.0
NA A:NA1009 4.9 50.8 1.0
N A:LYS38 4.9 35.6 1.0
CA A:LYS38 5.0 35.1 1.0

Fluorine binding site 2 out of 10 in 4tw9

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Fluorine binding site 2 out of 10 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 Fluorine with other atoms in the F 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:F1010

b:60.4
occ:1.00
 F4 A:3861010 0.0 60.4 1.0
C19 A:3861010 1.4 58.2 1.0
O5 A:3861010 2.2 56.9 1.0
F5 A:3861010 2.3 69.0 1.0
O4 A:3861010 2.3 56.4 1.0
O A:HOH1146 2.7 20.6 1.0
OH A:TYR56 2.7 20.5 1.0
C16 A:3861010 3.2 47.5 1.0
C15 A:3861010 3.2 47.3 1.0
CZ A:TYR56 3.4 31.0 1.0
CE2 A:TYR56 3.8 34.1 1.0
CB A:ILE148 3.9 33.9 1.0
CG A:MET82 4.1 40.3 1.0
CG2 A:ILE148 4.1 36.2 1.0
CE1 A:TYR56 4.3 30.1 1.0
CE A:MET80 4.3 36.5 1.0
CE A:MET82 4.4 38.4 1.0
C18 A:3861010 4.5 43.9 1.0
C17 A:3861010 4.5 42.8 1.0
N A:ASP149 4.6 37.2 1.0
CB A:MET82 4.7 37.2 1.0
NA A:NA1009 4.7 50.8 1.0
CA A:ILE148 4.8 33.9 1.0
SD A:MET82 4.8 43.9 1.0
CD1 A:ILE148 4.8 20.7 1.0
CG A:PRO66 4.9 30.2 1.0
CB A:PRO66 4.9 30.8 1.0
CD2 A:TYR56 4.9 37.4 1.0
CG1 A:ILE148 5.0 29.2 1.0

Fluorine binding site 3 out of 10 in 4tw9

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Fluorine binding site 3 out of 10 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 Fluorine with other atoms in the F 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
A:F1010

b:67.4
occ:1.00
 F3 A:3861010 0.0 67.4 1.0
C7 A:3861010 1.4 70.9 1.0
F2 A:3861010 2.2 75.7 1.0
O1 A:3861010 2.3 79.1 1.0
F1 A:3861010 2.3 65.0 1.0
C3 A:3861010 3.5 81.0 1.0
O2 A:3861010 3.5 76.4 1.0
CG A:PRO87 3.8 42.9 1.0
CD1 A:LEU293 3.8 45.0 1.0
C8 A:3861010 4.0 76.2 1.0
CB A:PRO87 4.1 42.5 1.0
C1 A:3861010 4.2 81.5 1.0
CD2 A:LEU92 4.3 40.9 1.0
CE2 A:PHE295 4.3 59.3 1.0
C5 A:3861010 4.5 82.8 1.0
O A:HOH1185 4.6 47.9 1.0
CZ A:PHE295 4.6 55.9 1.0
CD A:PRO87 4.8 44.3 1.0
N1 A:3861010 4.9 63.3 1.0

Fluorine binding site 4 out of 10 in 4tw9

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Fluorine binding site 4 out of 10 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 Fluorine with other atoms in the F 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
A:F1010

b:75.7
occ:1.00
 F2 A:3861010 0.0 75.7 1.0
C7 A:3861010 1.3 70.9 1.0
F1 A:3861010 2.1 65.0 1.0
O1 A:3861010 2.2 79.1 1.0
F3 A:3861010 2.2 67.4 1.0
C3 A:3861010 2.6 81.0 1.0
CB A:PRO87 2.7 42.5 1.0
C8 A:3861010 2.8 76.2 1.0
C1 A:3861010 2.8 81.5 1.0
O2 A:3861010 3.1 76.4 1.0
CG A:PRO87 3.2 42.9 1.0
N1 A:3861010 3.4 63.3 1.0
CB A:ASP91 3.4 42.0 1.0
C5 A:3861010 3.6 82.8 1.0
C2 A:3861010 4.0 83.3 1.0
OD2 A:ASP91 4.0 49.3 1.0
CA A:PRO87 4.2 41.9 1.0
CG A:ASP91 4.2 45.3 1.0
C9 A:3861010 4.3 64.7 1.0
C A:ASP91 4.4 41.1 1.0
N A:LEU92 4.4 39.8 1.0
CD A:PRO87 4.5 44.3 1.0
CA A:ASP91 4.5 42.0 1.0
C6 A:3861010 4.5 86.7 1.0
C4 A:3861010 4.7 86.3 1.0
CD2 A:LEU92 4.7 40.9 1.0
O A:ASP91 4.8 41.5 1.0
CG A:LEU92 4.8 38.9 1.0
O A:HOH1185 4.8 47.9 1.0
N A:PRO87 4.9 42.9 1.0
C A:PRO87 4.9 40.0 1.0
CA A:LEU92 5.0 38.0 1.0

Fluorine binding site 5 out of 10 in 4tw9

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Fluorine binding site 5 out of 10 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 Fluorine with other atoms in the F binding site number 5 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:F1010

b:65.0
occ:1.00
 F1 A:3861010 0.0 65.0 1.0
C7 A:3861010 1.4 70.9 1.0
F2 A:3861010 2.1 75.7 1.0
O1 A:3861010 2.3 79.1 1.0
F3 A:3861010 2.3 67.4 1.0
C3 A:3861010 3.0 81.0 1.0
C5 A:3861010 3.3 82.8 1.0
CB A:PHE95 3.5 41.5 1.0
O A:ASP91 3.5 41.5 1.0
C A:ASP91 3.6 41.1 1.0
N A:LEU92 3.7 39.8 1.0
CA A:LEU92 3.9 38.0 1.0
CB A:ASP91 4.0 42.0 1.0
C1 A:3861010 4.0 81.5 1.0
CG A:PHE95 4.1 45.0 1.0
CD2 A:LEU92 4.1 40.9 1.0
CA A:ASP91 4.4 42.0 1.0
CG A:LEU92 4.5 38.9 1.0
C6 A:3861010 4.5 86.7 1.0
C8 A:3861010 4.6 76.2 1.0
CB A:PRO87 4.6 42.5 1.0
CD1 A:PHE95 4.6 45.8 1.0
CG A:PRO87 4.7 42.9 1.0
CD2 A:PHE95 4.7 44.7 1.0
O2 A:3861010 4.7 76.4 1.0
CA A:PHE95 4.8 41.5 1.0
CB A:LEU92 4.8 37.6 1.0
O A:HOH1185 4.9 47.9 1.0
N A:PHE95 4.9 40.1 1.0
CD1 A:LEU293 4.9 45.0 1.0
C A:LEU92 5.0 36.3 1.0

Fluorine binding site 6 out of 10 in 4tw9

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Fluorine binding site 6 out of 10 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 Fluorine with other atoms in the F binding site number 6 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:F1007

b:68.1
occ:1.00
 F5 B:3861007 0.0 68.1 1.0
C19 B:3861007 1.4 56.7 1.0
F4 B:3861007 2.2 59.6 1.0
O4 B:3861007 2.3 53.4 1.0
O5 B:3861007 2.3 50.1 1.0
C15 B:3861007 3.1 45.7 1.0
C16 B:3861007 3.1 43.1 1.0
CG B:MET82 3.3 36.1 1.0
CE B:MET80 3.5 19.7 1.0
O B:HOH1193 3.5 17.4 1.0
CD B:LYS38 4.0 29.2 1.0
CB B:MET82 4.2 35.0 1.0
CD1 B:ILE23 4.2 37.5 1.0
CB B:LYS38 4.3 30.9 1.0
C17 B:3861007 4.3 47.5 1.0
SD B:MET82 4.4 34.8 1.0
C18 B:3861007 4.4 44.3 1.0
OH B:TYR56 4.4 32.8 1.0
CE2 B:TYR56 4.6 30.6 1.0
CG B:LYS38 4.7 30.1 1.0
CZ B:TYR56 4.8 28.1 1.0
NA B:NA1006 4.9 44.1 1.0

Fluorine binding site 7 out of 10 in 4tw9

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Fluorine binding site 7 out of 10 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 Fluorine with other atoms in the F binding site number 7 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:F1007

b:59.6
occ:1.00
 F4 B:3861007 0.0 59.6 1.0
C19 B:3861007 1.4 56.7 1.0
F5 B:3861007 2.2 68.1 1.0
O4 B:3861007 2.3 53.4 1.0
O5 B:3861007 2.3 50.1 1.0
OH B:TYR56 2.5 32.8 1.0
O B:HOH1193 2.7 17.4 1.0
CZ B:TYR56 3.0 28.1 1.0
C15 B:3861007 3.2 45.7 1.0
C16 B:3861007 3.2 43.1 1.0
CE2 B:TYR56 3.5 30.6 1.0
CE1 B:TYR56 3.8 28.9 1.0
CG2 B:ILE148 4.1 33.2 1.0
CG B:MET82 4.1 36.1 1.0
CG B:PRO66 4.1 27.1 1.0
CB B:ILE148 4.2 32.1 1.0
CE B:MET80 4.5 19.7 1.0
C17 B:3861007 4.5 47.5 1.0
CD2 B:TYR56 4.5 34.9 1.0
C18 B:3861007 4.5 44.3 1.0
CE B:MET82 4.5 38.1 1.0
N B:ASP149 4.7 34.5 1.0
SD B:MET82 4.7 34.8 1.0
CD1 B:TYR56 4.7 29.4 1.0
CA B:ILE148 4.8 31.6 1.0
OE2 B:GLU52 4.8 35.4 1.0
CB B:PRO66 4.8 31.1 1.0
CB B:MET82 4.9 35.0 1.0

Fluorine binding site 8 out of 10 in 4tw9

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Fluorine binding site 8 out of 10 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 Fluorine with other atoms in the F binding site number 8 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:F1007

b:71.0
occ:1.00
 F3 B:3861007 0.0 71.0 1.0
C7 B:3861007 1.4 68.9 1.0
F2 B:3861007 2.2 70.0 1.0
F1 B:3861007 2.3 74.1 1.0
O1 B:3861007 2.3 63.1 1.0
C3 B:3861007 3.1 69.5 1.0
O2 B:3861007 3.2 72.8 1.0
CD1 B:LEU293 3.6 49.3 1.0
C1 B:3861007 3.8 70.7 1.0
C8 B:3861007 3.8 73.1 1.0
C5 B:3861007 3.9 72.1 1.0
CG B:PRO87 4.8 37.9 1.0
C5 A:HSJ1005 4.8 84.6 1.0
C2 B:3861007 4.9 71.8 1.0
CB B:PRO87 4.9 37.8 1.0
CD2 B:LEU92 5.0 32.2 1.0
C3 A:HSJ1005 5.0 84.9 1.0

Fluorine binding site 9 out of 10 in 4tw9

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Fluorine binding site 9 out of 10 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 Fluorine with other atoms in the F binding site number 9 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:F1007

b:70.0
occ:1.00
 F2 B:3861007 0.0 70.0 1.0
C7 B:3861007 1.4 68.9 1.0
F1 B:3861007 2.2 74.1 1.0
F3 B:3861007 2.2 71.0 1.0
O1 B:3861007 2.3 63.1 1.0
CD2 B:LEU92 2.9 32.2 1.0
CD1 B:LEU293 3.3 49.3 1.0
C3 B:3861007 3.5 69.5 1.0
CG B:LEU92 4.1 36.1 1.0
C5 B:3861007 4.1 72.1 1.0
CG B:PRO87 4.1 37.9 1.0
CB B:PRO87 4.4 37.8 1.0
O2 B:3861007 4.4 72.8 1.0
CB B:PHE95 4.5 46.1 1.0
CG B:PHE95 4.6 42.5 1.0
C1 B:3861007 4.6 70.7 1.0
CA B:LEU92 4.6 35.7 1.0
CG B:LEU293 4.6 52.0 1.0
CD2 B:PHE95 4.7 42.9 1.0
O B:ASP91 4.8 35.4 1.0
C8 B:3861007 4.8 73.1 1.0
N B:LEU92 4.9 35.3 1.0
CB B:LEU92 4.9 35.2 1.0
C B:ASP91 4.9 36.0 1.0

Fluorine binding site 10 out of 10 in 4tw9

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Fluorine binding site 10 out of 10 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 Fluorine with other atoms in the F binding site number 10 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:F1007

b:74.1
occ:1.00
 F1 B:3861007 0.0 74.1 1.0
C7 B:3861007 1.3 68.9 1.0
O1 B:3861007 2.2 63.1 1.0
F2 B:3861007 2.2 70.0 1.0
F3 B:3861007 2.3 71.0 1.0
C5 B:3861007 2.5 72.1 1.0
C3 B:3861007 2.6 69.5 1.0
C6 B:3861007 3.8 71.6 1.0
C1 B:3861007 3.8 70.7 1.0
CB B:PHE95 4.0 46.1 1.0
CG B:PHE95 4.1 42.5 1.0
CD1 B:PHE95 4.1 43.6 1.0
C7 A:HSJ1005 4.2 88.8 1.0
C5 A:HSJ1005 4.2 84.6 1.0
C6 A:HSJ1005 4.4 84.9 1.0
O B:ASP91 4.4 35.4 1.0
CD1 B:LEU293 4.5 49.3 1.0
O2 B:3861007 4.5 72.8 1.0
C8 B:3861007 4.6 73.1 1.0
C4 B:3861007 4.7 73.9 1.0
C2 B:3861007 4.7 71.8 1.0
CD2 B:LEU92 4.8 32.2 1.0
CD2 B:PHE95 4.9 42.9 1.0
CE1 B:PHE95 4.9 43.8 1.0
C B:ASP91 5.0 36.0 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: Sun Dec 13 12:12:34 2020

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