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Fluorine in PDB 4pmp: The Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea

Enzymatic activity of The Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea

All present enzymatic activity of The Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea:
2.7.10.1;

Protein crystallography data

The structure of The Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea, PDB code: 4pmp was solved by H.P.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.86 / 1.80
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 75.543, 75.543, 112.508, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 18.5

Other elements in 4pmp:

The structure of The Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea (pdb code 4pmp). 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 Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea, PDB code: 4pmp:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4pmp

Go back to Fluorine Binding Sites List in 4pmp
Fluorine binding site 1 out of 3 in the The Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:44.3
occ:1.00
 F2 A:31W801 0.0 44.3 1.0
C18 A:31W801 1.3 45.0 1.0
F A:31W801 2.1 43.3 1.0
F1 A:31W801 2.1 46.7 1.0
O A:31W801 2.2 44.0 1.0
C17 A:31W801 2.9 44.9 1.0
C19 A:31W801 3.1 45.6 1.0
O A:HOH927 3.3 58.2 1.0
CD2 A:HIS648 3.8 19.0 1.0
NE2 A:HIS648 3.8 17.9 1.0
C16 A:31W801 4.0 43.0 1.0
CB A:ASP668 4.0 28.7 1.0
O A:GLY667 4.1 22.7 1.0
CE2 A:PHE646 4.3 24.0 1.0
C20 A:31W801 4.3 44.6 1.0
C A:GLY667 4.4 26.4 1.0
CZ A:PHE646 4.5 23.4 1.0
OD1 A:ASP668 4.6 51.1 1.0
CD1 A:LEU567 4.6 38.1 1.0
CG A:HIS648 4.7 17.2 1.0
CE1 A:HIS648 4.8 17.8 1.0
CG A:ASP668 4.8 47.3 1.0
N A:ASP668 4.9 26.4 1.0
CG2 A:ILE666 4.9 18.4 1.0
C15 A:31W801 5.0 42.1 1.0

Fluorine binding site 2 out of 3 in 4pmp

Go back to Fluorine Binding Sites List in 4pmp
Fluorine binding site 2 out of 3 in the The Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:46.7
occ:1.00
 F1 A:31W801 0.0 46.7 1.0
C18 A:31W801 1.3 45.0 1.0
F A:31W801 2.1 43.3 1.0
F2 A:31W801 2.1 44.3 1.0
O A:31W801 2.2 44.0 1.0
C17 A:31W801 2.8 44.9 1.0
C16 A:31W801 3.1 43.0 1.0
CG2 A:ILE666 3.5 18.4 1.0
O A:GLY667 3.5 22.7 1.0
O A:ILE666 3.6 20.1 1.0
CA A:GLY667 3.7 19.7 1.0
C A:GLY667 3.7 26.4 1.0
C19 A:31W801 3.7 45.6 1.0
C A:ILE666 3.8 18.2 1.0
N A:GLY667 3.9 16.9 1.0
CD2 A:HIS648 4.2 19.0 1.0
NE2 A:HIS648 4.2 17.9 1.0
CG2 A:ILE572 4.3 21.6 1.0
C15 A:31W801 4.3 42.1 1.0
CB A:ILE666 4.3 15.5 1.0
CD1 A:ILE572 4.4 29.1 1.0
N A:ASP668 4.5 26.4 1.0
C20 A:31W801 4.7 44.6 1.0
CA A:ILE666 4.7 12.7 1.0
CB A:ASP668 4.8 28.7 1.0
C14 A:31W801 4.9 42.4 1.0
CD1 A:LEU641 5.0 19.9 1.0

Fluorine binding site 3 out of 3 in 4pmp

Go back to Fluorine Binding Sites List in 4pmp
Fluorine binding site 3 out of 3 in the The Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Structure of Trka Kinase Bound to the Inhibitor 1-Cyclopropyl-1- [3-(1,3-Thiazol-2-Yl)Benzyl]-3-[4-(Trifluoromethoxy)Phenyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:43.3
occ:1.00
 F A:31W801 0.0 43.3 1.0
C18 A:31W801 1.3 45.0 1.0
F2 A:31W801 2.1 44.3 1.0
F1 A:31W801 2.1 46.7 1.0
O A:31W801 2.2 44.0 1.0
CD1 A:LEU567 3.3 38.1 1.0
C17 A:31W801 3.5 44.9 1.0
CD2 A:LEU641 4.0 18.2 1.0
CD1 A:LEU641 4.0 19.9 1.0
CE2 A:PHE646 4.1 24.0 1.0
CD1 A:ILE572 4.2 29.1 1.0
CG2 A:ILE572 4.3 21.6 1.0
C16 A:31W801 4.3 43.0 1.0
C19 A:31W801 4.4 45.6 1.0
CZ A:PHE646 4.5 23.4 1.0
CD2 A:HIS648 4.5 19.0 1.0
CG A:LEU641 4.6 18.6 1.0
CG A:LEU567 4.6 37.8 1.0
CD2 A:PHE646 4.8 21.0 1.0
CG2 A:ILE666 4.8 18.4 1.0
CG1 A:ILE572 5.0 21.4 1.0

Reference:

S.J.Stachel, J.M.Sanders, D.A.Henze, M.T.Rudd, H.P.Su, Y.Li, K.K.Nanda, M.S.Egbertson, P.J.Manley, K.L.Jones, E.J.Brnardic, A.Green, J.A.Grobler, B.Hanney, M.Leitl, M.T.Lai, V.Munshi, D.Murphy, K.Rickert, D.Riley, A.Krasowska-Zoladek, C.Daley, P.Zuck, S.A.Kane, M.T.Bilodeau. Maximizing Diversity From A Kinase Screen: Identification of Novel and Selective Pan-Trk Inhibitors For Chronic Pain. J.Med.Chem. V. 57 5800 2014.
ISSN: ISSN 0022-2623
PubMed: 24914455
DOI: 10.1021/JM5006429
Page generated: Tue Jul 15 00:09:26 2025

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