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Fluorine in PDB 7xaf: The Crystal Structure of Trka Kinase in Complex with 4^6,14-Dimethyl- N-(3-(4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-10-Oxo-5- Oxa-11,14-Diaza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)-Benzenacyclo- Tetradecaphan-2-Yne-45-Carboxamide

Enzymatic activity of The Crystal Structure of Trka Kinase in Complex with 4^6,14-Dimethyl- N-(3-(4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-10-Oxo-5- Oxa-11,14-Diaza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)-Benzenacyclo- Tetradecaphan-2-Yne-45-Carboxamide

All present enzymatic activity of The Crystal Structure of Trka Kinase in Complex with 4^6,14-Dimethyl- N-(3-(4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-10-Oxo-5- Oxa-11,14-Diaza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)-Benzenacyclo- Tetradecaphan-2-Yne-45-Carboxamide:
2.7.10.1;

Protein crystallography data

The structure of The Crystal Structure of Trka Kinase in Complex with 4^6,14-Dimethyl- N-(3-(4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-10-Oxo-5- Oxa-11,14-Diaza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)-Benzenacyclo- Tetradecaphan-2-Yne-45-Carboxamide, PDB code: 7xaf was solved by Z.M.Zhang, Y.J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.41 / 3.00
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 52.116, 52.116, 228.483, 90, 90, 120
R / Rfree (%) 24.4 / 29.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Crystal Structure of Trka Kinase in Complex with 4^6,14-Dimethyl- N-(3-(4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-10-Oxo-5- Oxa-11,14-Diaza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)-Benzenacyclo- Tetradecaphan-2-Yne-45-Carboxamide (pdb code 7xaf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the The Crystal Structure of Trka Kinase in Complex with 4^6,14-Dimethyl- N-(3-(4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-10-Oxo-5- Oxa-11,14-Diaza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)-Benzenacyclo- Tetradecaphan-2-Yne-45-Carboxamide, PDB code: 7xaf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7xaf

Go back to Fluorine Binding Sites List in 7xaf
Fluorine binding site 1 out of 3 in the The Crystal Structure of Trka Kinase in Complex with 4^6,14-Dimethyl- N-(3-(4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-10-Oxo-5- Oxa-11,14-Diaza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)-Benzenacyclo- Tetradecaphan-2-Yne-45-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Crystal Structure of Trka Kinase in Complex with 4^6,14-Dimethyl- N-(3-(4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-10-Oxo-5- Oxa-11,14-Diaza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)-Benzenacyclo- Tetradecaphan-2-Yne-45-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:61.4
occ:1.00
 F47 A:FKT801 0.0 61.4 1.0
C46 A:FKT801 1.3 54.5 1.0
F49 A:FKT801 2.2 57.4 1.0
F48 A:FKT801 2.2 44.6 1.0
C38 A:FKT801 2.4 62.1 1.0
C39 A:FKT801 2.8 56.0 1.0
O A:ILE666 3.3 19.1 1.0
CG2 A:ILE572 3.5 12.7 1.0
C37 A:FKT801 3.7 65.0 1.0
C34 A:FKT801 4.2 61.8 1.0
C A:ILE666 4.3 24.7 1.0
O33 A:FKT801 4.4 51.3 1.0
CG2 A:ILE666 4.5 23.4 1.0
CB A:ILE666 4.6 14.7 1.0
CD1 A:ILE572 4.7 14.1 1.0
CB A:ILE572 4.8 12.8 1.0
C36 A:FKT801 4.8 65.9 1.0
N A:VAL573 4.9 11.5 1.0
CD1 A:LEU567 4.9 26.4 1.0

Fluorine binding site 2 out of 3 in 7xaf

Go back to Fluorine Binding Sites List in 7xaf
Fluorine binding site 2 out of 3 in the The Crystal Structure of Trka Kinase in Complex with 4^6,14-Dimethyl- N-(3-(4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-10-Oxo-5- Oxa-11,14-Diaza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)-Benzenacyclo- Tetradecaphan-2-Yne-45-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Crystal Structure of Trka Kinase in Complex with 4^6,14-Dimethyl- N-(3-(4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-10-Oxo-5- Oxa-11,14-Diaza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)-Benzenacyclo- Tetradecaphan-2-Yne-45-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:44.6
occ:1.00
 F48 A:FKT801 0.0 44.6 1.0
C46 A:FKT801 1.3 54.5 1.0
F49 A:FKT801 2.2 57.4 1.0
F47 A:FKT801 2.2 61.4 1.0
C38 A:FKT801 2.4 62.1 1.0
C37 A:FKT801 2.8 65.0 1.0
CD1 A:LEU567 3.1 26.4 1.0
C39 A:FKT801 3.6 56.0 1.0
C36 A:FKT801 4.2 65.9 1.0
CG2 A:ILE572 4.3 12.7 1.0
CE1 A:PHE646 4.3 36.8 1.0
CZ A:PHE646 4.4 40.5 1.0
CG A:LEU567 4.4 22.4 1.0
CD2 A:LEU641 4.5 13.0 1.0
CB A:LEU567 4.7 20.3 1.0
C34 A:FKT801 4.7 61.8 1.0
CD1 A:LEU641 4.7 17.8 1.0
C35 A:FKT801 5.0 70.0 1.0
CD1 A:PHE646 5.0 33.0 1.0
CD2 A:HIS648 5.0 27.8 1.0

Fluorine binding site 3 out of 3 in 7xaf

Go back to Fluorine Binding Sites List in 7xaf
Fluorine binding site 3 out of 3 in the The Crystal Structure of Trka Kinase in Complex with 4^6,14-Dimethyl- N-(3-(4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-10-Oxo-5- Oxa-11,14-Diaza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)-Benzenacyclo- Tetradecaphan-2-Yne-45-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Crystal Structure of Trka Kinase in Complex with 4^6,14-Dimethyl- N-(3-(4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-10-Oxo-5- Oxa-11,14-Diaza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)-Benzenacyclo- Tetradecaphan-2-Yne-45-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:57.4
occ:1.00
 F49 A:FKT801 0.0 57.4 1.0
C46 A:FKT801 1.3 54.5 1.0
F47 A:FKT801 2.2 61.4 1.0
F48 A:FKT801 2.2 44.6 1.0
C38 A:FKT801 2.4 62.1 1.0
C37 A:FKT801 3.1 65.0 1.0
CD2 A:HIS648 3.1 27.8 1.0
C39 A:FKT801 3.3 56.0 1.0
NE2 A:HIS648 3.5 25.3 1.0
CG2 A:ILE666 4.0 23.4 1.0
CG A:HIS648 4.3 29.3 1.0
O A:ILE666 4.4 19.1 1.0
C36 A:FKT801 4.4 65.9 1.0
CD1 A:LEU641 4.5 17.8 1.0
C34 A:FKT801 4.5 61.8 1.0
CB A:ILE666 4.6 14.7 1.0
CE2 A:PHE669 4.7 61.8 1.0
CE1 A:HIS648 4.7 27.3 1.0
CE1 A:PHE646 4.7 36.8 1.0
O A:ASP668 4.9 55.0 1.0
C35 A:FKT801 5.0 70.0 1.0

Reference:

Z.Wang, J.Wang, Y.Wang, S.Xiang, X.Song, Z.Tu, Y.Zhou, Z.M.Zhang, Z.Zhang, K.Ding, X.Lu. Discovery of the First Highly Selective and Broadly Effective Macrocycle-Based Type II Trk Inhibitors That Overcome Clinically Acquired Resistance. J.Med.Chem. V. 65 6325 2022.
ISSN: ISSN 0022-2623
PubMed: 35426680
DOI: 10.1021/ACS.JMEDCHEM.2C00308
Page generated: Wed Jul 16 01:50:36 2025

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