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Fluorine in PDB 7mgk: TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea

Enzymatic activity of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea

All present enzymatic activity of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea:
2.7.11.1;

Protein crystallography data

The structure of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea, PDB code: 7mgk was solved by L.M.Shewchuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.51 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.673, 75.072, 95.235, 83.28, 85.95, 74.79
R / Rfree (%) 19.6 / 23.9

Other elements in 7mgk:

The structure of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea (pdb code 7mgk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea, PDB code: 7mgk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 7mgk

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Fluorine binding site 1 out of 12 in the TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:68.5
occ:1.00
 F35 A:ZGD801 0.0 68.5 1.0
C34 A:ZGD801 1.3 53.9 1.0
F37 A:ZGD801 2.2 54.9 1.0
F36 A:ZGD801 2.2 51.2 1.0
C31 A:ZGD801 2.3 46.6 1.0
C29 A:ZGD801 2.7 45.4 1.0
CD1 A:LEU577 3.2 42.2 1.0
CD2 A:LEU577 3.3 43.5 1.0
C32 A:ZGD801 3.5 51.2 1.0
CD1 A:LEU516 3.5 47.0 1.0
CG A:LEU577 3.9 44.3 1.0
C27 A:ZGD801 4.1 56.8 1.0
CG1 A:VAL521 4.4 42.5 1.0
CG2 A:ILE584 4.5 39.0 1.0
C24 A:ZGD801 4.6 50.6 1.0
CD2 A:LEU516 4.6 44.0 1.0
CG A:LEU516 4.7 49.4 1.0
CD1 A:ILE584 4.8 50.6 1.0
CG2 A:ILE512 4.8 55.2 1.0
CD2 A:HIS586 4.9 40.0 1.0
C25 A:ZGD801 4.9 52.0 1.0

Fluorine binding site 2 out of 12 in 7mgk

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Fluorine binding site 2 out of 12 in the TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:51.2
occ:1.00
 F36 A:ZGD801 0.0 51.2 1.0
C34 A:ZGD801 1.3 53.9 1.0
F37 A:ZGD801 2.2 54.9 1.0
F35 A:ZGD801 2.2 68.5 1.0
C31 A:ZGD801 2.3 46.6 1.0
C32 A:ZGD801 2.7 51.2 1.0
O A:VAL604 3.4 40.6 1.0
CG1 A:VAL521 3.5 42.5 1.0
C29 A:ZGD801 3.6 45.4 1.0
CD1 A:LEU516 3.6 47.0 1.0
CG2 A:ILE522 3.8 43.1 1.0
CA A:ALA605 4.1 39.5 1.0
C24 A:ZGD801 4.1 50.6 1.0
C A:VAL604 4.1 40.6 1.0
C A:ALA605 4.4 42.9 1.0
CG1 A:VAL604 4.4 35.5 1.0
N A:ALA605 4.4 43.3 1.0
N A:ILE522 4.5 42.7 1.0
O21 A:ZGD801 4.5 48.1 1.0
CB A:ILE522 4.6 41.6 1.0
CD1 A:LEU577 4.7 42.2 1.0
CD2 A:LEU577 4.7 43.5 1.0
O A:ALA605 4.7 46.9 1.0
C27 A:ZGD801 4.7 56.8 1.0
CB A:VAL521 4.8 35.3 1.0
C25 A:ZGD801 4.9 52.0 1.0
N A:ASP606 4.9 49.2 1.0
CB A:VAL604 5.0 37.9 1.0
N22 A:ZGD801 5.0 50.6 1.0

Fluorine binding site 3 out of 12 in 7mgk

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Fluorine binding site 3 out of 12 in the TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:54.9
occ:1.00
 F37 A:ZGD801 0.0 54.9 1.0
C34 A:ZGD801 1.3 53.9 1.0
F35 A:ZGD801 2.2 68.5 1.0
F36 A:ZGD801 2.2 51.2 1.0
C31 A:ZGD801 2.3 46.6 1.0
C29 A:ZGD801 3.0 45.4 1.0
C32 A:ZGD801 3.2 51.2 1.0
CD2 A:HIS586 3.2 40.0 1.0
NE2 A:HIS586 3.5 46.2 1.0
O A:ALA605 3.6 46.9 1.0
CG1 A:VAL604 3.8 35.5 1.0
C A:ALA605 3.9 42.9 1.0
CD1 A:LEU577 4.0 42.2 1.0
CG A:HIS586 4.1 43.0 1.0
CB A:ASP606 4.2 48.8 1.0
CA A:ALA605 4.2 39.5 1.0
C27 A:ZGD801 4.3 56.8 1.0
CE1 A:HIS586 4.4 44.5 1.0
O A:VAL604 4.4 40.6 1.0
C24 A:ZGD801 4.4 50.6 1.0
N A:ALA605 4.4 43.3 1.0
N A:ASP606 4.5 49.2 1.0
C A:VAL604 4.5 40.6 1.0
ND1 A:HIS586 4.7 40.7 1.0
C25 A:ZGD801 4.9 52.0 1.0
CB A:HIS586 4.9 46.0 1.0
CB A:VAL604 4.9 37.9 1.0
CA A:ASP606 5.0 49.3 1.0

Fluorine binding site 4 out of 12 in 7mgk

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Fluorine binding site 4 out of 12 in the TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:55.9
occ:1.00
 F35 B:ZGD801 0.0 55.9 1.0
C34 B:ZGD801 1.3 47.1 1.0
F37 B:ZGD801 2.2 50.9 1.0
F36 B:ZGD801 2.2 48.1 1.0
C31 B:ZGD801 2.3 41.8 1.0
C29 B:ZGD801 2.7 44.9 1.0
CD1 B:LEU577 3.3 45.9 1.0
CD2 B:LEU577 3.4 39.6 1.0
C32 B:ZGD801 3.5 45.5 1.0
CD1 B:LEU516 3.7 49.7 1.0
CG B:LEU577 4.0 44.3 1.0
C27 B:ZGD801 4.1 50.4 1.0
CG2 B:ILE512 4.3 54.1 1.0
CG1 B:VAL521 4.5 44.0 1.0
CD2 B:LEU516 4.6 49.5 1.0
C24 B:ZGD801 4.6 51.8 1.0
CG2 B:ILE584 4.6 42.8 1.0
CD2 B:HIS586 4.8 47.3 1.0
CG B:LEU516 4.8 48.6 1.0
CD1 B:ILE584 4.8 49.5 1.0
C25 B:ZGD801 4.9 50.5 1.0

Fluorine binding site 5 out of 12 in 7mgk

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Fluorine binding site 5 out of 12 in the TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:48.1
occ:1.00
 F36 B:ZGD801 0.0 48.1 1.0
C34 B:ZGD801 1.3 47.1 1.0
F37 B:ZGD801 2.2 50.9 1.0
F35 B:ZGD801 2.2 55.9 1.0
C31 B:ZGD801 2.3 41.8 1.0
C32 B:ZGD801 2.7 45.5 1.0
CD1 B:LEU516 3.2 49.7 1.0
CG1 B:VAL521 3.3 44.0 1.0
C29 B:ZGD801 3.6 44.9 1.0
CG2 B:ILE522 3.6 47.8 1.0
O B:VAL604 3.7 36.2 1.0
C24 B:ZGD801 4.0 51.8 1.0
CA B:ALA605 4.4 34.2 1.0
C B:VAL604 4.5 35.6 1.0
CD2 B:LEU577 4.6 39.6 1.0
N B:ILE522 4.6 39.5 1.0
CG B:LEU516 4.6 48.6 1.0
CB B:ILE522 4.7 42.4 1.0
C27 B:ZGD801 4.7 50.4 1.0
CD1 B:LEU577 4.7 45.9 1.0
CB B:VAL521 4.7 36.2 1.0
O21 B:ZGD801 4.7 48.5 1.0
C B:ALA605 4.8 41.2 1.0
N B:ALA605 4.8 31.5 1.0
CD2 B:LEU513 4.8 48.4 1.0
C25 B:ZGD801 4.9 50.5 1.0
CG1 B:VAL604 4.9 35.1 1.0
N22 B:ZGD801 4.9 53.4 1.0

Fluorine binding site 6 out of 12 in 7mgk

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Fluorine binding site 6 out of 12 in the TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:50.9
occ:1.00
 F37 B:ZGD801 0.0 50.9 1.0
C34 B:ZGD801 1.3 47.1 1.0
F36 B:ZGD801 2.2 48.1 1.0
F35 B:ZGD801 2.2 55.9 1.0
C31 B:ZGD801 2.3 41.8 1.0
C29 B:ZGD801 3.1 44.9 1.0
C32 B:ZGD801 3.2 45.5 1.0
CD2 B:HIS586 3.4 47.3 1.0
NE2 B:HIS586 3.5 48.2 1.0
O B:ALA605 3.5 41.1 1.0
CG1 B:VAL604 3.7 35.1 1.0
C B:ALA605 3.7 41.2 1.0
CA B:ALA605 3.9 34.2 1.0
CD1 B:LEU577 3.9 45.9 1.0
O B:VAL604 4.0 36.2 1.0
N B:ALA605 4.2 31.5 1.0
C B:VAL604 4.2 35.6 1.0
CB B:ASP606 4.3 42.5 1.0
C27 B:ZGD801 4.4 50.4 1.0
C24 B:ZGD801 4.4 51.8 1.0
N B:ASP606 4.4 45.1 1.0
CG B:HIS586 4.5 45.6 1.0
CE1 B:HIS586 4.6 48.3 1.0
CB B:VAL604 4.7 35.9 1.0
C25 B:ZGD801 4.9 50.5 1.0
CG1 B:VAL521 4.9 44.0 1.0
O21 B:ZGD801 4.9 48.5 1.0
CD2 B:LEU577 5.0 39.6 1.0

Fluorine binding site 7 out of 12 in 7mgk

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Fluorine binding site 7 out of 12 in the TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:61.4
occ:1.00
 F35 C:ZGD801 0.0 61.4 1.0
C34 C:ZGD801 1.3 59.4 1.0
F36 C:ZGD801 2.2 60.4 1.0
F37 C:ZGD801 2.2 55.4 1.0
C31 C:ZGD801 2.3 53.0 1.0
C29 C:ZGD801 2.7 46.1 1.0
CD1 C:LEU577 3.2 36.9 1.0
C32 C:ZGD801 3.6 52.9 1.0
CD2 C:LEU577 3.8 45.5 1.0
CD1 C:LEU516 3.9 50.8 1.0
C27 C:ZGD801 4.0 56.3 1.0
CG C:LEU577 4.1 40.7 1.0
CD2 C:HIS586 4.4 45.9 1.0
CG2 C:ILE584 4.6 37.9 1.0
CG1 C:VAL521 4.7 44.3 1.0
C24 C:ZGD801 4.7 53.8 1.0
C25 C:ZGD801 4.9 58.7 1.0
NE2 C:HIS586 5.0 46.0 1.0
CD2 C:LEU516 5.0 41.7 1.0

Fluorine binding site 8 out of 12 in 7mgk

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Fluorine binding site 8 out of 12 in the TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:60.4
occ:1.00
 F36 C:ZGD801 0.0 60.4 1.0
C34 C:ZGD801 1.3 59.4 1.0
F37 C:ZGD801 2.2 55.4 1.0
F35 C:ZGD801 2.2 61.4 1.0
C31 C:ZGD801 2.3 53.0 1.0
C32 C:ZGD801 2.8 52.9 1.0
CD1 C:LEU516 3.2 50.8 1.0
CG1 C:VAL521 3.3 44.3 1.0
C29 C:ZGD801 3.5 46.1 1.0
CG2 C:ILE522 3.7 51.3 1.0
O C:VAL604 3.8 50.3 1.0
C24 C:ZGD801 4.1 53.8 1.0
CA C:ALA605 4.4 42.6 1.0
CD1 C:LEU577 4.6 36.9 1.0
C C:VAL604 4.6 45.9 1.0
C27 C:ZGD801 4.6 56.3 1.0
N C:ILE522 4.6 46.3 1.0
CG C:LEU516 4.7 46.7 1.0
CD2 C:LEU577 4.7 45.5 1.0
O21 C:ZGD801 4.7 51.1 1.0
CB C:VAL521 4.7 41.8 1.0
C C:ALA605 4.7 48.0 1.0
CB C:ILE522 4.7 54.8 1.0
C25 C:ZGD801 4.9 58.7 1.0
N C:ALA605 4.9 45.5 1.0
CG1 C:VAL604 5.0 38.5 1.0

Fluorine binding site 9 out of 12 in 7mgk

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Fluorine binding site 9 out of 12 in the TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:55.4
occ:1.00
 F37 C:ZGD801 0.0 55.4 1.0
C34 C:ZGD801 1.3 59.4 1.0
F36 C:ZGD801 2.2 60.4 1.0
F35 C:ZGD801 2.2 61.4 1.0
C31 C:ZGD801 2.3 53.0 1.0
C32 C:ZGD801 3.0 52.9 1.0
C29 C:ZGD801 3.3 46.1 1.0
O C:ALA605 3.4 54.5 1.0
CD2 C:HIS586 3.4 45.9 1.0
NE2 C:HIS586 3.5 46.0 1.0
C C:ALA605 3.5 48.0 1.0
CA C:ALA605 3.8 42.6 1.0
CB C:ASP606 3.8 54.0 1.0
N C:ASP606 4.0 54.0 1.0
CG1 C:VAL604 4.1 38.5 1.0
O C:VAL604 4.1 50.3 1.0
N C:ALA605 4.2 45.5 1.0
C24 C:ZGD801 4.3 53.8 1.0
C C:VAL604 4.3 45.9 1.0
CG C:HIS586 4.4 45.5 1.0
CE1 C:HIS586 4.4 48.1 1.0
CD1 C:LEU577 4.4 36.9 1.0
C27 C:ZGD801 4.5 56.3 1.0
CA C:ASP606 4.6 55.7 1.0
O21 C:ZGD801 4.6 51.1 1.0
C25 C:ZGD801 4.9 58.7 1.0
ND1 C:HIS586 4.9 50.4 1.0
CG C:ASP606 4.9 61.9 1.0

Fluorine binding site 10 out of 12 in 7mgk

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Fluorine binding site 10 out of 12 in the TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of TNNI3K Complexed with 1-(3,5-Dichloro-4-((6-(Methylamino)Pyrimidin-4- Yl)Oxy)Phenyl)-3-(3-(Trifluoromethyl)Phenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F801

b:58.7
occ:1.00
 F35 D:ZGD801 0.0 58.7 1.0
C34 D:ZGD801 1.3 58.7 1.0
F37 D:ZGD801 2.2 59.9 1.0
F36 D:ZGD801 2.2 61.7 1.0
C31 D:ZGD801 2.3 54.3 1.0
C29 D:ZGD801 2.7 57.4 1.0
CD1 D:LEU577 3.3 51.4 1.0
CD2 D:LEU577 3.3 61.7 1.0
C32 D:ZGD801 3.6 54.0 1.0
CG D:LEU577 3.9 53.8 1.0
C27 D:ZGD801 4.0 60.2 1.0
CD1 D:LEU516 4.1 54.0 1.0
CD2 D:HIS586 4.5 52.8 1.0
CG1 D:VAL521 4.6 49.4 1.0
CG2 D:ILE512 4.6 60.5 1.0
CG2 D:ILE584 4.7 46.9 1.0
C24 D:ZGD801 4.7 57.2 1.0
CD2 D:LEU516 4.9 55.0 1.0
C25 D:ZGD801 4.9 56.6 1.0
CB D:LEU577 5.0 50.2 1.0
CD1 D:ILE584 5.0 62.8 1.0

Reference:

J.R.Patterson, A.P.Graves, P.Stoy, M.Cheung, T.A.Desai, H.Fries, G.J.Gatto Jr., D.A.Holt, L.Shewchuk, R.Totoritis, L.Wang, L.S.Kallander. Identification of Diarylurea Inhibitors of the Cardiac-Specific Kinase TNNI3K By Designing Selectivity Against VEGFR2, P38 Alpha , and B-Raf. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34699203
DOI: 10.1021/ACS.JMEDCHEM.1C00700
Page generated: Tue Jul 15 21:40:00 2025

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