Fluorine in PDB 8j61: The Crystal Structure of Trka Kinase in Complex with 4^6-Methyl-N-(3- (4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-14-Oxo-5-Oxa- 13-Aza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)- Benzenacyclotetradecaphan-2-Yne-4^5-Carboxamide

Enzymatic activity of The Crystal Structure of Trka Kinase in Complex with 4^6-Methyl-N-(3- (4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-14-Oxo-5-Oxa- 13-Aza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)- Benzenacyclotetradecaphan-2-Yne-4^5-Carboxamide

All present enzymatic activity of The Crystal Structure of Trka Kinase in Complex with 4^6-Methyl-N-(3- (4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-14-Oxo-5-Oxa- 13-Aza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)- Benzenacyclotetradecaphan-2-Yne-4^5-Carboxamide:
2.7.10.1;

Protein crystallography data

The structure of The Crystal Structure of Trka Kinase in Complex with 4^6-Methyl-N-(3- (4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-14-Oxo-5-Oxa- 13-Aza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)- Benzenacyclotetradecaphan-2-Yne-4^5-Carboxamide, PDB code: 8j61 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) 25.86 / 3.05
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 51.729, 51.729, 228.592, 90, 90, 120
R / Rfree (%) 20.4 / 25.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Crystal Structure of Trka Kinase in Complex with 4^6-Methyl-N-(3- (4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-14-Oxo-5-Oxa- 13-Aza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)- Benzenacyclotetradecaphan-2-Yne-4^5-Carboxamide (pdb code 8j61). 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-Methyl-N-(3- (4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-14-Oxo-5-Oxa- 13-Aza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)- Benzenacyclotetradecaphan-2-Yne-4^5-Carboxamide, PDB code: 8j61:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8j61

Go back to Fluorine Binding Sites List in 8j61
Fluorine binding site 1 out of 3 in the The Crystal Structure of Trka Kinase in Complex with 4^6-Methyl-N-(3- (4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-14-Oxo-5-Oxa- 13-Aza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)- Benzenacyclotetradecaphan-2-Yne-4^5-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-Methyl-N-(3- (4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-14-Oxo-5-Oxa- 13-Aza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)- Benzenacyclotetradecaphan-2-Yne-4^5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:131.7
occ:1.00
 F46 A:A0X801 0.0 131.7 1.0
C45 A:A0X801 1.3 127.6 1.0
F47 A:A0X801 2.2 124.9 1.0
F48 A:A0X801 2.2 127.2 1.0
C24 A:A0X801 2.4 126.9 1.0
C25 A:A0X801 2.8 123.4 1.0
C23 A:A0X801 3.5 127.3 1.0
CD2 A:LEU564 3.6 35.1 1.0
CG2 A:ILE572 3.9 29.4 1.0
CA A:GLY667 4.0 60.4 1.0
O A:ILE666 4.1 31.0 1.0
C20 A:A0X801 4.2 122.3 1.0
CD1 A:LEU567 4.3 76.7 1.0
N A:ASP668 4.4 95.8 1.0
C A:GLY667 4.5 74.2 1.0
C22 A:A0X801 4.7 123.3 1.0
C A:ILE666 4.8 29.8 1.0
N A:GLY667 4.9 56.0 1.0
C21 A:A0X801 4.9 125.2 1.0
O19 A:A0X801 4.9 113.7 1.0

Fluorine binding site 2 out of 3 in 8j61

Go back to Fluorine Binding Sites List in 8j61
Fluorine binding site 2 out of 3 in the The Crystal Structure of Trka Kinase in Complex with 4^6-Methyl-N-(3- (4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-14-Oxo-5-Oxa- 13-Aza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)- Benzenacyclotetradecaphan-2-Yne-4^5-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-Methyl-N-(3- (4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-14-Oxo-5-Oxa- 13-Aza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)- Benzenacyclotetradecaphan-2-Yne-4^5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:124.9
occ:1.00
 F47 A:A0X801 0.0 124.9 1.0
C45 A:A0X801 1.3 127.6 1.0
F46 A:A0X801 2.2 131.7 1.0
F48 A:A0X801 2.2 127.2 1.0
C24 A:A0X801 2.3 126.9 1.0
C23 A:A0X801 2.7 127.3 1.0
CD1 A:LEU567 3.3 76.7 1.0
C25 A:A0X801 3.6 123.4 1.0
C22 A:A0X801 4.1 123.3 1.0
CD2 A:LEU564 4.5 35.1 1.0
CB A:ASP668 4.7 107.8 1.0
C20 A:A0X801 4.7 122.3 1.0
CG A:LEU567 4.8 70.8 1.0
C21 A:A0X801 4.9 125.2 1.0
N26 A:A0X801 4.9 118.4 1.0
N A:ASP668 5.0 95.8 1.0

Fluorine binding site 3 out of 3 in 8j61

Go back to Fluorine Binding Sites List in 8j61
Fluorine binding site 3 out of 3 in the The Crystal Structure of Trka Kinase in Complex with 4^6-Methyl-N-(3- (4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-14-Oxo-5-Oxa- 13-Aza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)- Benzenacyclotetradecaphan-2-Yne-4^5-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-Methyl-N-(3- (4-Methyl-1H-Imidazol-1-Yl)-5-(Trifluoromethyl)Phenyl)-14-Oxo-5-Oxa- 13-Aza-1(3,6)-Imidazo[1,2-B]Pyridazina-4(1,3)- Benzenacyclotetradecaphan-2-Yne-4^5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:127.2
occ:1.00
 F48 A:A0X801 0.0 127.2 1.0
C45 A:A0X801 1.3 127.6 1.0
F46 A:A0X801 2.2 131.7 1.0
F47 A:A0X801 2.2 124.9 1.0
C24 A:A0X801 2.3 126.9 1.0
C A:GLY667 3.0 74.2 1.0
N A:ASP668 3.1 95.8 1.0
C25 A:A0X801 3.1 123.4 1.0
CA A:GLY667 3.2 60.4 1.0
C23 A:A0X801 3.3 127.3 1.0
CB A:ASP668 3.5 107.8 1.0
O A:GLY667 3.5 69.7 1.0
NE2 A:HIS648 3.7 31.0 1.0
CA A:ASP668 3.8 99.1 1.0
N A:GLY667 4.0 56.0 1.0
O A:ILE666 4.1 31.0 1.0
C A:ILE666 4.3 29.8 1.0
CD2 A:HIS648 4.3 30.0 1.0
C20 A:A0X801 4.3 122.3 1.0
CG2 A:ILE666 4.5 29.5 1.0
C22 A:A0X801 4.5 123.3 1.0
CE1 A:HIS648 4.6 35.5 1.0
O19 A:A0X801 4.7 113.7 1.0
CG A:ASP668 4.9 113.3 1.0
C21 A:A0X801 4.9 125.2 1.0

Reference:

Z.Wang, J.Wang, Y.Wang, S.Xiang, H.Zhou, S.Song, X.Song, Z.Tu, Y.Zhou, K.Ding, Z.M.Zhang, Z.Zhang, X.Lu. Structure-Based Optimization of the Third Generation Type II Macrocycle Trk Inhibitors with Improved Activity Against Solvent-Front, Xdfg, and Gatekeeper Mutations. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37676745
DOI: 10.1021/ACS.JMEDCHEM.3C00899
Page generated: Fri Aug 2 20:53:30 2024

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