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Fluorine in PDB 6dkw: Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3.

Enzymatic activity of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3.

All present enzymatic activity of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3.:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3., PDB code: 6dkw was solved by S.E.Greasley, D.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.39 / 2.91
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.980, 93.980, 159.270, 90.00, 90.00, 120.00
R / Rfree (%) 23.1 / 26.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3. (pdb code 6dkw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3., PDB code: 6dkw:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6dkw

Go back to Fluorine Binding Sites List in 6dkw
Fluorine binding site 1 out of 6 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3.


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 Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:77.5
occ:1.00
 F1 A:GXA801 0.0 77.5 1.0
C25 A:GXA801 1.3 75.5 1.0
F3 A:GXA801 2.1 75.9 1.0
F2 A:GXA801 2.1 78.6 1.0
O4 A:GXA801 2.2 70.8 1.0
H23 A:GXA801 2.7 65.0 1.0
C22 A:GXA801 2.8 67.2 1.0
C21 A:GXA801 3.0 65.3 1.0
NE2 A:HIS648 3.1 68.0 1.0
CD2 A:HIS648 3.1 68.4 1.0
O A:GLY667 3.6 68.3 1.0
C A:GLY667 4.0 67.6 1.0
C23 A:GXA801 4.0 66.5 1.0
CE1 A:PHE646 4.2 74.0 1.0
CB A:ASP668 4.2 67.2 1.0
CE1 A:HIS648 4.2 67.5 1.0
C20 A:GXA801 4.3 65.2 1.0
CG A:HIS648 4.3 67.0 1.0
CZ A:PHE646 4.3 72.2 1.0
H24 A:GXA801 4.4 66.4 1.0
CA A:GLY667 4.4 60.7 1.0
N A:ASP668 4.6 64.9 1.0
O A:ILE666 4.8 62.9 1.0
CG2 A:ILE666 4.8 62.7 1.0
OD2 A:ASP668 4.8 89.5 1.0
H22 A:GXA801 4.9 65.2 1.0
ND1 A:HIS648 4.9 68.3 1.0
N A:GLY667 4.9 60.1 1.0

Fluorine binding site 2 out of 6 in 6dkw

Go back to Fluorine Binding Sites List in 6dkw
Fluorine binding site 2 out of 6 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3.


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 Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:78.6
occ:1.00
 F2 A:GXA801 0.0 78.6 1.0
C25 A:GXA801 1.3 75.5 1.0
F1 A:GXA801 2.1 77.5 1.0
F3 A:GXA801 2.1 75.9 1.0
O4 A:GXA801 2.2 70.8 1.0
C22 A:GXA801 2.8 67.2 1.0
O A:ILE666 2.9 62.9 1.0
H24 A:GXA801 3.1 66.4 1.0
C23 A:GXA801 3.2 66.5 1.0
C A:ILE666 3.5 63.1 1.0
CG2 A:ILE572 3.6 65.0 1.0
CA A:GLY667 3.7 60.7 1.0
C21 A:GXA801 3.7 65.3 1.0
N A:GLY667 3.9 60.1 1.0
O A:GLY667 3.9 68.3 1.0
H23 A:GXA801 4.0 65.0 1.0
C A:GLY667 4.0 67.6 1.0
CG2 A:ILE666 4.0 62.7 1.0
CD1 A:ILE572 4.1 63.2 1.0
CD2 A:HIS648 4.3 68.4 1.0
NE2 A:HIS648 4.3 68.0 1.0
CB A:ILE666 4.3 62.8 1.0
C24 A:GXA801 4.4 65.4 1.0
CA A:ILE666 4.6 59.2 1.0
CB A:ILE572 4.6 64.0 1.0
C20 A:GXA801 4.7 65.2 1.0
CD1 A:LEU641 4.8 76.3 1.0
CG1 A:ILE572 4.9 62.5 1.0
CD2 A:LEU641 4.9 74.4 1.0
N A:ASP668 4.9 64.9 1.0
CA A:ILE572 5.0 61.9 1.0

Fluorine binding site 3 out of 6 in 6dkw

Go back to Fluorine Binding Sites List in 6dkw
Fluorine binding site 3 out of 6 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3.


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 Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:75.9
occ:1.00
 F3 A:GXA801 0.0 75.9 1.0
C25 A:GXA801 1.3 75.5 1.0
F1 A:GXA801 2.1 77.5 1.0
F2 A:GXA801 2.1 78.6 1.0
O4 A:GXA801 2.1 70.8 1.0
CD2 A:LEU641 3.4 74.4 1.0
CE1 A:PHE646 3.4 74.0 1.0
C22 A:GXA801 3.5 67.2 1.0
CD1 A:LEU567 3.7 76.1 1.0
CZ A:PHE646 3.7 72.2 1.0
CD1 A:LEU641 3.9 76.3 1.0
CD2 A:HIS648 4.1 68.4 1.0
H23 A:GXA801 4.2 65.0 1.0
CD1 A:PHE646 4.2 74.1 1.0
H24 A:GXA801 4.2 66.4 1.0
CG2 A:ILE572 4.3 65.0 1.0
C21 A:GXA801 4.3 65.3 1.0
CG A:LEU641 4.3 76.2 1.0
C23 A:GXA801 4.3 66.5 1.0
CD1 A:ILE572 4.5 63.2 1.0
CE2 A:PHE646 4.6 74.2 1.0
NE2 A:HIS648 4.6 68.0 1.0
CG A:LEU567 4.8 76.7 1.0
O A:ILE666 4.9 62.9 1.0

Fluorine binding site 4 out of 6 in 6dkw

Go back to Fluorine Binding Sites List in 6dkw
Fluorine binding site 4 out of 6 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:82.9
occ:1.00
 F1 B:GXA801 0.0 82.9 1.0
C25 B:GXA801 1.3 76.2 1.0
O4 B:GXA801 2.1 71.5 1.0
F3 B:GXA801 2.1 76.9 1.0
F2 B:GXA801 2.2 72.4 1.0
H23 B:GXA801 2.7 59.0 1.0
C22 B:GXA801 2.8 65.6 1.0
C21 B:GXA801 3.0 60.1 1.0
NE2 B:HIS648 3.3 67.5 1.0
CD2 B:HIS648 3.4 68.0 1.0
C23 B:GXA801 4.0 65.2 1.0
O B:GLY667 4.0 59.8 1.0
CE1 B:PHE646 4.1 78.1 1.0
C B:GLY667 4.2 64.3 1.0
CB B:ASP668 4.3 64.2 1.0
C20 B:GXA801 4.3 60.4 1.0
CZ B:PHE646 4.3 77.5 1.0
CE1 B:HIS648 4.3 67.4 1.0
H24 B:GXA801 4.3 65.7 1.0
O B:HOH925 4.3 92.0 1.0
CG B:HIS648 4.4 66.7 1.0
CD1 B:LEU567 4.5 91.3 1.0
CA B:GLY667 4.7 64.2 1.0
N B:ASP668 4.7 62.1 1.0
H22 B:GXA801 4.8 60.5 1.0
ND1 B:HIS648 4.9 68.6 1.0

Fluorine binding site 5 out of 6 in 6dkw

Go back to Fluorine Binding Sites List in 6dkw
Fluorine binding site 5 out of 6 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:72.4
occ:1.00
 F2 B:GXA801 0.0 72.4 1.0
C25 B:GXA801 1.3 76.2 1.0
O4 B:GXA801 2.1 71.5 1.0
F3 B:GXA801 2.1 76.9 1.0
F1 B:GXA801 2.2 82.9 1.0
C22 B:GXA801 2.5 65.6 1.0
H24 B:GXA801 2.9 65.7 1.0
C23 B:GXA801 2.9 65.2 1.0
O B:ILE666 3.2 67.1 1.0
CA B:GLY667 3.4 64.2 1.0
C21 B:GXA801 3.4 60.1 1.0
C B:ILE666 3.5 69.1 1.0
C B:GLY667 3.6 64.3 1.0
N B:GLY667 3.6 65.4 1.0
O B:GLY667 3.6 59.8 1.0
H23 B:GXA801 3.7 59.0 1.0
CG2 B:ILE572 3.9 79.8 1.0
C24 B:GXA801 4.0 62.2 1.0
NE2 B:HIS648 4.0 67.5 1.0
CD2 B:HIS648 4.2 68.0 1.0
CG2 B:ILE666 4.3 69.0 1.0
C20 B:GXA801 4.4 60.4 1.0
CB B:ILE666 4.4 69.9 1.0
N B:ASP668 4.4 62.1 1.0
CD1 B:ILE572 4.6 87.0 1.0
CA B:ILE666 4.6 67.5 1.0
C19 B:GXA801 4.6 59.5 1.0
H25 B:GXA801 4.7 62.0 1.0
CB B:ILE572 4.9 79.2 1.0

Fluorine binding site 6 out of 6 in 6dkw

Go back to Fluorine Binding Sites List in 6dkw
Fluorine binding site 6 out of 6 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 3. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:76.9
occ:1.00
 F3 B:GXA801 0.0 76.9 1.0
C25 B:GXA801 1.3 76.2 1.0
F2 B:GXA801 2.1 72.4 1.0
F1 B:GXA801 2.1 82.9 1.0
O4 B:GXA801 2.2 71.5 1.0
C22 B:GXA801 3.5 65.6 1.0
CD2 B:LEU641 3.5 81.3 1.0
CD1 B:LEU641 3.7 81.4 1.0
CD1 B:LEU567 3.9 91.3 1.0
CG2 B:ILE572 3.9 79.8 1.0
CD2 B:HIS648 4.0 68.0 1.0
CE1 B:PHE646 4.0 78.1 1.0
H24 B:GXA801 4.1 65.7 1.0
CD1 B:ILE572 4.1 87.0 1.0
C23 B:GXA801 4.2 65.2 1.0
CG B:LEU641 4.3 81.0 1.0
H23 B:GXA801 4.4 59.0 1.0
C21 B:GXA801 4.4 60.1 1.0
NE2 B:HIS648 4.4 67.5 1.0
CZ B:PHE646 4.5 77.5 1.0
CD1 B:PHE646 4.6 77.5 1.0
CG1 B:ILE572 4.8 79.2 1.0
O B:ILE666 4.8 67.1 1.0
CG B:LEU567 4.8 90.8 1.0
CD2 B:LEU567 4.9 89.8 1.0
CB B:ILE572 4.9 79.2 1.0

Reference:

S.K.Bagal, M.Andrews, B.M.Bechle, J.Bian, J.Bilsland, D.C.Blakemore, J.F.Braganza, P.J.Bungay, M.S.Corbett, C.N.Cronin, J.J.Cui, R.Dias, N.J.Flanagan, S.E.Greasley, R.Grimley, K.James, E.Johnson, L.Kitching, M.L.Kraus, I.Mcalpine, A.Nagata, S.Ninkovic, K.Omoto, S.Scales, S.E.Skerratt, J.Sun, M.Tran-Dube, G.J.Waldron, F.Wang, J.S.Warmus. Discovery of Potent, Selective, and Peripherally Restricted Pan-Trk Kinase Inhibitors For the Treatment of Pain. J. Med. Chem. V. 61 6779 2018.
ISSN: ISSN 1520-4804
PubMed: 29944371
DOI: 10.1021/ACS.JMEDCHEM.8B00633
Page generated: Tue Jul 15 10:48:33 2025

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