Chlorine 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:

Fluorine (F) 12 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 8 in 7mgk

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Chlorine binding site 1 out of 8 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 Chlorine with other atoms in the Cl 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:Cl801

b:78.0
occ:1.00
 CL14 A:ZGD801 0.0 78.0 1.0
C13 A:ZGD801 1.7 48.7 1.0
C15 A:ZGD801 2.7 49.1 1.0
C12 A:ZGD801 2.8 44.5 1.0
O11 A:ZGD801 3.1 40.2 1.0
OG1 A:THR539 3.3 45.2 1.0
O A:ALA488 3.5 44.3 1.0
CB A:ALA488 3.5 37.5 1.0
C A:ALA488 3.7 42.5 1.0
C10 A:ZGD801 3.9 41.3 1.0
N A:LYS490 4.0 46.5 1.0
N42 A:ZGD801 4.0 41.1 1.0
C17 A:ZGD801 4.0 47.5 1.0
C40 A:ZGD801 4.0 46.0 1.0
CB A:LYS490 4.1 49.5 1.0
N A:ILE489 4.1 43.1 1.0
C A:ILE489 4.1 44.0 1.0
O A:ILE537 4.2 42.6 1.0
CA A:ALA488 4.3 45.3 1.0
CG1 A:VAL477 4.3 41.4 1.0
CG2 A:THR539 4.4 46.5 1.0
CA A:ILE489 4.4 45.6 1.0
CB A:THR539 4.4 46.3 1.0
CA A:LYS490 4.5 48.3 1.0
C38 A:ZGD801 4.5 42.8 1.0
O A:ILE489 4.6 47.8 1.0
N A:THR539 4.8 36.5 1.0
CG A:LYS490 4.8 58.8 1.0
CD A:LYS490 4.9 61.9 1.0

Chlorine binding site 2 out of 8 in 7mgk

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Chlorine binding site 2 out of 8 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 Chlorine with other atoms in the Cl 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:Cl801

b:63.4
occ:1.00
 CL41 A:ZGD801 0.0 63.4 1.0
C40 A:ZGD801 1.7 46.0 1.0
C38 A:ZGD801 2.7 42.8 1.0
C12 A:ZGD801 2.7 44.5 1.0
O11 A:ZGD801 3.0 40.2 1.0
CZ A:PHE607 3.2 57.2 1.0
C10 A:ZGD801 3.3 41.3 1.0
CE1 A:PHE607 3.4 50.5 1.0
CE2 A:PHE607 3.4 58.5 1.0
CB A:ALA605 3.6 33.1 1.0
CD1 A:PHE607 3.7 54.7 1.0
N42 A:ZGD801 3.7 41.1 1.0
CD2 A:PHE607 3.8 61.9 1.0
C08 A:ZGD801 3.8 33.1 1.0
CD1 A:LEU595 3.9 33.2 1.0
CG A:PHE607 4.0 60.5 1.0
C17 A:ZGD801 4.0 47.5 1.0
C13 A:ZGD801 4.0 48.7 1.0
C15 A:ZGD801 4.5 49.1 1.0
N A:ASP606 4.6 49.2 1.0
CD1 A:ILE522 4.6 35.4 1.0
C43 A:ZGD801 4.6 38.7 1.0
CG A:LEU595 4.6 40.2 1.0
N A:PHE607 4.7 52.4 1.0
C07 A:ZGD801 4.7 38.3 1.0
CA A:PHE607 4.8 57.8 1.0
C A:ASP606 4.8 53.1 1.0
O21 A:ZGD801 4.9 48.1 1.0
CA A:ALA605 5.0 39.5 1.0

Chlorine binding site 3 out of 8 in 7mgk

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Chlorine binding site 3 out of 8 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 Chlorine with other atoms in the Cl 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
B:Cl801

b:84.3
occ:1.00
 CL14 B:ZGD801 0.0 84.3 1.0
C13 B:ZGD801 1.7 56.5 1.0
C15 B:ZGD801 2.7 57.3 1.0
C12 B:ZGD801 2.8 51.6 1.0
O11 B:ZGD801 3.1 54.8 1.0
CB B:LYS490 3.4 50.1 1.0
N B:LYS490 3.5 44.5 1.0
O B:ALA488 3.7 47.1 1.0
OG1 B:THR539 3.7 42.6 1.0
C B:ILE489 3.9 44.9 1.0
CA B:LYS490 3.9 49.3 1.0
C B:ALA488 3.9 48.1 1.0
C17 B:ZGD801 4.0 51.8 1.0
C10 B:ZGD801 4.0 52.0 1.0
O B:ILE537 4.0 49.5 1.0
CB B:ALA488 4.0 47.4 1.0
C40 B:ZGD801 4.0 53.9 1.0
CG1 B:VAL477 4.1 44.8 1.0
CG B:LYS490 4.2 51.4 1.0
N B:ILE489 4.2 49.2 1.0
N42 B:ZGD801 4.2 53.6 1.0
CA B:ILE489 4.3 47.2 1.0
O B:ILE489 4.4 51.2 1.0
C38 B:ZGD801 4.5 49.8 1.0
CA B:ALA488 4.6 47.1 1.0
CG2 B:THR539 4.7 49.4 1.0
CB B:THR539 4.8 47.4 1.0
CG2 B:VAL477 5.0 55.0 1.0

Chlorine binding site 4 out of 8 in 7mgk

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Chlorine binding site 4 out of 8 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 Chlorine with other atoms in the Cl 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:Cl801

b:76.0
occ:1.00
 CL41 B:ZGD801 0.0 76.0 1.0
C40 B:ZGD801 1.7 53.9 1.0
C38 B:ZGD801 2.7 49.8 1.0
C12 B:ZGD801 2.8 51.6 1.0
O11 B:ZGD801 3.0 54.8 1.0
C10 B:ZGD801 3.1 52.0 1.0
CZ B:PHE607 3.2 52.4 1.0
CE1 B:PHE607 3.3 49.0 1.0
CD1 B:LEU595 3.3 47.8 1.0
N42 B:ZGD801 3.5 53.6 1.0
CB B:ALA605 3.7 35.9 1.0
CE2 B:PHE607 3.7 56.1 1.0
C08 B:ZGD801 3.7 51.4 1.0
CD1 B:PHE607 3.8 54.3 1.0
C17 B:ZGD801 4.0 51.8 1.0
C13 B:ZGD801 4.0 56.5 1.0
CD2 B:PHE607 4.2 58.4 1.0
CG B:PHE607 4.2 59.1 1.0
C43 B:ZGD801 4.2 49.7 1.0
CG B:LEU595 4.3 42.9 1.0
C07 B:ZGD801 4.5 49.1 1.0
C15 B:ZGD801 4.5 57.3 1.0
N45 B:ZGD801 4.7 48.4 1.0
CD2 B:LEU595 4.7 41.5 1.0
N B:ASP606 4.8 45.1 1.0
O21 B:ZGD801 4.8 48.5 1.0
CD1 B:ILE522 5.0 52.6 1.0
N B:PHE607 5.0 49.0 1.0

Chlorine binding site 5 out of 8 in 7mgk

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Chlorine binding site 5 out of 8 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 Chlorine with other atoms in the Cl 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
C:Cl801

b:90.9
occ:1.00
 CL14 C:ZGD801 0.0 90.9 1.0
C13 C:ZGD801 1.7 61.1 1.0
C15 C:ZGD801 2.7 58.9 1.0
C12 C:ZGD801 2.7 55.6 1.0
O11 C:ZGD801 3.0 57.0 1.0
OG1 C:THR539 3.3 51.4 1.0
CB C:ALA488 3.4 63.4 1.0
O C:ALA488 3.6 57.4 1.0
C10 C:ZGD801 3.6 56.8 1.0
N42 C:ZGD801 3.6 55.8 1.0
C C:ALA488 3.7 63.1 1.0
N C:LYS490 4.0 75.8 1.0
C40 C:ZGD801 4.0 59.5 1.0
C17 C:ZGD801 4.0 53.2 1.0
CB C:LYS490 4.1 78.5 1.0
CG1 C:VAL477 4.1 77.7 1.0
N C:ILE489 4.1 72.5 1.0
C C:ILE489 4.2 73.5 1.0
CA C:ALA488 4.2 64.4 1.0
O C:ILE537 4.4 61.2 1.0
CG2 C:THR539 4.4 52.7 1.0
CB C:THR539 4.4 53.2 1.0
CA C:LYS490 4.4 77.8 1.0
CA C:ILE489 4.5 71.2 1.0
C38 C:ZGD801 4.5 52.6 1.0
O C:ILE489 4.6 75.1 1.0
N C:THR539 4.7 56.4 1.0
C43 C:ZGD801 4.8 59.2 1.0
C08 C:ZGD801 4.8 52.6 1.0
CG C:LYS490 4.8 80.0 1.0

Chlorine binding site 6 out of 8 in 7mgk

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Chlorine binding site 6 out of 8 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 Chlorine with other atoms in the Cl 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
C:Cl801

b:85.6
occ:1.00
 CL41 C:ZGD801 0.0 85.6 1.0
C40 C:ZGD801 1.7 59.5 1.0
C38 C:ZGD801 2.7 52.6 1.0
C12 C:ZGD801 2.7 55.6 1.0
O11 C:ZGD801 3.0 57.0 1.0
CZ C:PHE607 3.3 73.0 1.0
CE2 C:PHE607 3.3 68.3 1.0
C10 C:ZGD801 3.4 56.8 1.0
CE1 C:PHE607 3.5 69.4 1.0
CD2 C:PHE607 3.6 68.2 1.0
CD1 C:LEU595 3.6 50.0 1.0
CD1 C:PHE607 3.7 68.4 1.0
CG C:PHE607 3.8 70.0 1.0
CB C:ALA605 3.8 43.7 1.0
N42 C:ZGD801 4.0 55.8 1.0
C17 C:ZGD801 4.0 53.2 1.0
C13 C:ZGD801 4.0 61.1 1.0
C08 C:ZGD801 4.1 52.6 1.0
N C:PHE607 4.4 56.4 1.0
CG C:LEU595 4.4 46.4 1.0
CA C:PHE607 4.5 60.6 1.0
C15 C:ZGD801 4.5 58.9 1.0
N C:ASP606 4.5 54.0 1.0
C C:ASP606 4.6 57.9 1.0
CB C:PHE607 4.7 63.8 1.0
CD2 C:LEU595 4.7 47.0 1.0
O21 C:ZGD801 4.8 51.1 1.0
O C:ASP606 4.9 59.5 1.0
C43 C:ZGD801 4.9 59.2 1.0

Chlorine binding site 7 out of 8 in 7mgk

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Chlorine binding site 7 out of 8 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 Chlorine with other atoms in the Cl 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
D:Cl801

b:101.1
occ:1.00
 CL14 D:ZGD801 0.0 101.1 1.0
C13 D:ZGD801 1.7 76.7 1.0
C15 D:ZGD801 2.7 72.3 1.0
C12 D:ZGD801 2.8 72.2 1.0
O D:ALA488 3.0 63.1 1.0
O11 D:ZGD801 3.1 68.2 1.0
CB D:LYS490 3.4 72.0 1.0
N D:LYS490 3.6 57.9 1.0
C D:ALA488 3.6 61.8 1.0
OG1 D:THR539 3.8 65.2 1.0
C D:ILE489 3.9 62.1 1.0
CB D:ALA488 4.0 67.6 1.0
CA D:LYS490 4.0 62.6 1.0
C17 D:ZGD801 4.0 67.5 1.0
C10 D:ZGD801 4.0 70.7 1.0
C40 D:ZGD801 4.0 71.9 1.0
O D:ILE537 4.1 62.5 1.0
N D:ILE489 4.2 62.2 1.0
CA D:ILE489 4.3 62.7 1.0
N42 D:ZGD801 4.4 72.2 1.0
CG1 D:VAL477 4.4 57.9 1.0
CG D:LYS490 4.4 77.5 1.0
CA D:ALA488 4.4 65.6 1.0
O D:ILE489 4.4 66.3 1.0
C38 D:ZGD801 4.5 66.3 1.0
CD D:LYS490 4.5 72.8 1.0
CG2 D:THR539 4.5 66.5 1.0
CB D:THR539 4.7 62.8 1.0
N D:THR539 4.8 57.0 1.0
CG2 D:VAL477 5.0 73.8 1.0

Chlorine binding site 8 out of 8 in 7mgk

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Chlorine binding site 8 out of 8 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 Chlorine with other atoms in the Cl 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
D:Cl801

b:96.7
occ:1.00
 CL41 D:ZGD801 0.0 96.7 1.0
C40 D:ZGD801 1.7 71.9 1.0
C38 D:ZGD801 2.7 66.3 1.0
C12 D:ZGD801 2.7 72.2 1.0
O11 D:ZGD801 3.0 68.2 1.0
C10 D:ZGD801 3.1 70.7 1.0
CD1 D:LEU595 3.3 65.7 1.0
CZ D:PHE607 3.3 61.8 1.0
N42 D:ZGD801 3.3 72.2 1.0
CE1 D:PHE607 3.3 61.7 1.0
CB D:ALA605 3.6 47.0 1.0
CE2 D:PHE607 3.6 60.6 1.0
CD1 D:PHE607 3.7 63.3 1.0
C08 D:ZGD801 3.8 72.1 1.0
C17 D:ZGD801 4.0 67.5 1.0
CD2 D:PHE607 4.0 64.6 1.0
C13 D:ZGD801 4.0 76.7 1.0
CG D:PHE607 4.0 65.6 1.0
C43 D:ZGD801 4.1 73.0 1.0
CG D:LEU595 4.5 58.4 1.0
C15 D:ZGD801 4.5 72.3 1.0
C07 D:ZGD801 4.5 73.9 1.0
N D:ASP606 4.6 54.3 1.0
N45 D:ZGD801 4.7 72.8 1.0
N D:PHE607 4.7 61.3 1.0
O21 D:ZGD801 4.8 63.0 1.0
CD2 D:LEU595 4.9 58.5 1.0
CA D:PHE607 4.9 64.1 1.0
CA D:ALA605 5.0 44.7 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 30 00:29:33 2024

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