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Fluorine in PDB 6kzc: Crystal Structure of Trkc in Complex with 3-(Imidazo[1,2-A]Pyrazin-3- Ylethynyl)-2-Methyl-N-(3-((4- Methylpiperazin-1-Yl)Methyl)-5- (Trifluoromethyl)Phenyl)Benzamide

Enzymatic activity of Crystal Structure of Trkc in Complex with 3-(Imidazo[1,2-A]Pyrazin-3- Ylethynyl)-2-Methyl-N-(3-((4- Methylpiperazin-1-Yl)Methyl)-5- (Trifluoromethyl)Phenyl)Benzamide

All present enzymatic activity of Crystal Structure of Trkc in Complex with 3-(Imidazo[1,2-A]Pyrazin-3- Ylethynyl)-2-Methyl-N-(3-((4- Methylpiperazin-1-Yl)Methyl)-5- (Trifluoromethyl)Phenyl)Benzamide:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Trkc in Complex with 3-(Imidazo[1,2-A]Pyrazin-3- Ylethynyl)-2-Methyl-N-(3-((4- Methylpiperazin-1-Yl)Methyl)-5- (Trifluoromethyl)Phenyl)Benzamide, PDB code: 6kzc was solved by Z.M.Zhang, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.67 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.811, 54.405, 108.885, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Trkc in Complex with 3-(Imidazo[1,2-A]Pyrazin-3- Ylethynyl)-2-Methyl-N-(3-((4- Methylpiperazin-1-Yl)Methyl)-5- (Trifluoromethyl)Phenyl)Benzamide (pdb code 6kzc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Trkc in Complex with 3-(Imidazo[1,2-A]Pyrazin-3- Ylethynyl)-2-Methyl-N-(3-((4- Methylpiperazin-1-Yl)Methyl)-5- (Trifluoromethyl)Phenyl)Benzamide, PDB code: 6kzc:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6kzc

Go back to Fluorine Binding Sites List in 6kzc
Fluorine binding site 1 out of 3 in the Crystal Structure of Trkc in Complex with 3-(Imidazo[1,2-A]Pyrazin-3- Ylethynyl)-2-Methyl-N-(3-((4- Methylpiperazin-1-Yl)Methyl)-5- (Trifluoromethyl)Phenyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Trkc in Complex with 3-(Imidazo[1,2-A]Pyrazin-3- Ylethynyl)-2-Methyl-N-(3-((4- Methylpiperazin-1-Yl)Methyl)-5- (Trifluoromethyl)Phenyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:20.8
occ:1.00
 FBJ A:DZC901 0.0 20.8 1.0
CBB A:DZC901 1.3 19.3 1.0
FBL A:DZC901 2.2 21.1 1.0
FBK A:DZC901 2.2 22.4 1.0
CAZ A:DZC901 2.3 20.1 1.0
CBA A:DZC901 3.1 18.3 1.0
O A:GLY696 3.2 14.5 1.0
C A:GLY696 3.2 16.3 1.0
NE2 A:HIS677 3.2 17.0 1.0
CAY A:DZC901 3.3 14.8 1.0
CD2 A:HIS677 3.4 17.1 1.0
CA A:GLY696 3.6 15.2 1.0
CB A:ASP697 3.7 12.7 1.0
N A:ASP697 3.7 17.8 1.0
O A:ILE695 4.1 16.1 1.0
N A:GLY696 4.2 13.1 1.0
CG2 A:ILE695 4.2 16.1 1.0
CA A:ASP697 4.3 13.0 1.0
O A:HOH1009 4.3 27.9 1.0
C A:ILE695 4.3 16.0 1.0
CAV A:DZC901 4.4 18.3 1.0
CE1 A:HIS677 4.4 13.1 1.0
CAX A:DZC901 4.5 23.5 1.0
CG A:HIS677 4.7 16.0 1.0
OAU A:DZC901 4.8 17.0 1.0
CG A:ASP697 4.9 21.6 1.0
CAW A:DZC901 4.9 13.7 1.0
CE2 A:PHE675 4.9 17.4 1.0
OD2 A:ASP697 5.0 22.6 1.0

Fluorine binding site 2 out of 3 in 6kzc

Go back to Fluorine Binding Sites List in 6kzc
Fluorine binding site 2 out of 3 in the Crystal Structure of Trkc in Complex with 3-(Imidazo[1,2-A]Pyrazin-3- Ylethynyl)-2-Methyl-N-(3-((4- Methylpiperazin-1-Yl)Methyl)-5- (Trifluoromethyl)Phenyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Trkc in Complex with 3-(Imidazo[1,2-A]Pyrazin-3- Ylethynyl)-2-Methyl-N-(3-((4- Methylpiperazin-1-Yl)Methyl)-5- (Trifluoromethyl)Phenyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:22.4
occ:1.00
 FBK A:DZC901 0.0 22.4 1.0
CBB A:DZC901 1.3 19.3 1.0
FBJ A:DZC901 2.2 20.8 1.0
FBL A:DZC901 2.2 21.1 1.0
CAZ A:DZC901 2.3 20.1 1.0
CAY A:DZC901 2.7 14.8 1.0
CD2 A:LEU595 3.6 28.3 1.0
CBA A:DZC901 3.6 18.3 1.0
CE2 A:PHE675 3.7 17.4 1.0
CZ A:PHE675 3.8 20.4 1.0
CAX A:DZC901 4.1 23.5 1.0
CD2 A:LEU591 4.3 21.8 1.0
CD2 A:LEU592 4.3 23.7 1.0
CD2 A:HIS677 4.5 17.1 1.0
O A:HOH1009 4.5 27.9 1.0
CD2 A:PHE675 4.6 15.4 1.0
CG2 A:ILE600 4.7 14.7 1.0
CAV A:DZC901 4.8 18.3 1.0
CE1 A:PHE675 4.8 23.0 1.0
NE2 A:HIS677 4.8 17.0 1.0
CD2 A:LEU670 4.8 15.0 1.0
NBC A:DZC901 4.9 40.8 1.0
CAW A:DZC901 4.9 13.7 1.0
CG A:LEU591 4.9 24.3 1.0
CBD A:DZC901 5.0 56.7 1.0
CG A:LEU595 5.0 28.5 1.0

Fluorine binding site 3 out of 3 in 6kzc

Go back to Fluorine Binding Sites List in 6kzc
Fluorine binding site 3 out of 3 in the Crystal Structure of Trkc in Complex with 3-(Imidazo[1,2-A]Pyrazin-3- Ylethynyl)-2-Methyl-N-(3-((4- Methylpiperazin-1-Yl)Methyl)-5- (Trifluoromethyl)Phenyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Trkc in Complex with 3-(Imidazo[1,2-A]Pyrazin-3- Ylethynyl)-2-Methyl-N-(3-((4- Methylpiperazin-1-Yl)Methyl)-5- (Trifluoromethyl)Phenyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:21.1
occ:1.00
 FBL A:DZC901 0.0 21.1 1.0
CBB A:DZC901 1.3 19.3 1.0
FBJ A:DZC901 2.2 20.8 1.0
FBK A:DZC901 2.2 22.4 1.0
CAZ A:DZC901 2.3 20.1 1.0
CBA A:DZC901 2.8 18.3 1.0
CD2 A:LEU592 3.4 23.7 1.0
CG2 A:ILE600 3.5 14.7 1.0
CAY A:DZC901 3.6 14.8 1.0
O A:ILE695 3.6 16.1 1.0
CG2 A:VAL601 3.6 18.6 1.0
CA A:GLY696 4.0 15.2 1.0
CAV A:DZC901 4.2 18.3 1.0
C A:GLY696 4.4 16.3 1.0
C A:ILE695 4.4 16.0 1.0
OAU A:DZC901 4.6 17.0 1.0
N A:GLY696 4.6 13.1 1.0
CD2 A:LEU595 4.7 28.3 1.0
CAX A:DZC901 4.7 23.5 1.0
CG A:LEU592 4.8 20.3 1.0
N A:VAL601 4.8 14.9 1.0
N A:ASP697 4.8 17.8 1.0
O A:GLY696 4.8 14.5 1.0
CB A:ILE600 4.9 16.4 1.0
CAW A:DZC901 4.9 13.7 1.0

Reference:

S.Cui, Y.Wang, Y.Wang, X.Tang, X.Ren, L.Zhang, Y.Xu, Z.Zhang, Z.M.Zhang, X.Lu, K.Ding. Design, Synthesis and Biological Evaluation of 3-(Imidazo[1,2-A]Pyrazin-3-Ylethynyl)-2-Methylbenzamides As Potent and Selective Pan-Tropomyosin Receptor Kinase (Trk) Inhibitors. Eur.J.Med.Chem. V. 179 470 2019.
ISSN: ISSN 0223-5234
PubMed: 31271959
DOI: 10.1016/J.EJMECH.2019.06.064
Page generated: Thu Aug 1 21:54:25 2024

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