Fluorine in PDB 6dki: Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 19.

Enzymatic activity of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 19.

All present enzymatic activity of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 19.:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 19., PDB code: 6dki was solved by S.E.Greasley, E.Johnson, M.L.Kraus, C.N.Cronin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.73 / 2.11
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.640, 45.510, 79.320, 90.00, 126.56, 90.00
R / Rfree (%) 18.4 / 22.7

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 19. (pdb code 6dki). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 19., PDB code: 6dki:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 6dki

Go back to Fluorine Binding Sites List in 6dki
Fluorine binding site 1 out of 5 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 19.


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 19. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:40.6
occ:1.00
F26 A:GOD802 0.0 40.6 1.0
C25 A:GOD802 1.3 40.4 1.0
F28 A:GOD802 2.1 40.6 1.0
F27 A:GOD802 2.1 42.3 1.0
O24 A:GOD802 2.2 38.3 1.0
CD1 A:LEU567 3.5 43.5 1.0
C21 A:GOD802 3.5 29.6 1.0
CD2 A:LEU641 3.5 26.8 1.0
CD1 A:LEU641 3.7 28.8 1.0
CD1 A:ILE572 4.0 25.0 1.0
CE1 A:PHE646 4.0 43.1 1.0
CG2 A:ILE572 4.0 29.1 1.0
HC20 A:GOD802 4.1 28.6 1.0
CZ A:PHE646 4.2 43.0 1.0
CG A:LEU641 4.2 28.9 1.0
C20 A:GOD802 4.3 28.6 1.0
HC22 A:GOD802 4.3 25.4 1.0
C22 A:GOD802 4.4 26.1 1.0
CD2 A:HIS648 4.5 28.8 1.0
CD1 A:PHE646 4.7 42.5 1.0
CG A:LEU567 4.8 42.1 1.0
CG2 A:ILE666 4.8 25.6 1.0
CG1 A:ILE572 4.8 27.2 1.0
O A:ILE666 4.9 23.9 1.0

Fluorine binding site 2 out of 5 in 6dki

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Fluorine binding site 2 out of 5 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 19.


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 19. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:42.3
occ:1.00
F27 A:GOD802 0.0 42.3 1.0
C25 A:GOD802 1.3 40.4 1.0
F26 A:GOD802 2.1 40.6 1.0
F28 A:GOD802 2.1 40.6 1.0
O24 A:GOD802 2.2 38.3 1.0
C21 A:GOD802 2.8 29.6 1.0
O A:ILE666 3.3 23.9 1.0
C20 A:GOD802 3.5 28.6 1.0
CG2 A:ILE666 3.5 25.6 1.0
C A:ILE666 3.5 26.3 1.0
CA A:GLY667 3.5 24.0 1.0
C22 A:GOD802 3.6 26.1 1.0
O A:GLY667 3.6 26.7 1.0
HC20 A:GOD802 3.6 28.6 1.0
N A:GLY667 3.6 23.8 1.0
C A:GLY667 3.7 28.9 1.0
HC22 A:GOD802 3.7 25.4 1.0
CD2 A:HIS648 4.0 28.8 1.0
NE2 A:HIS648 4.0 27.8 1.0
CB A:ILE666 4.1 25.7 1.0
CG2 A:ILE572 4.3 29.1 1.0
CD1 A:ILE572 4.3 25.0 1.0
CA A:ILE666 4.4 22.6 1.0
C19 A:GOD802 4.5 28.1 1.0
C23 A:GOD802 4.6 28.9 1.0
CD1 A:LEU641 4.7 28.8 1.0
N A:ASP668 4.7 26.1 1.0

Fluorine binding site 3 out of 5 in 6dki

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Fluorine binding site 3 out of 5 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 19.


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 19. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:40.6
occ:1.00
F28 A:GOD802 0.0 40.6 1.0
C25 A:GOD802 1.3 40.4 1.0
F26 A:GOD802 2.1 40.6 1.0
F27 A:GOD802 2.1 42.3 1.0
O24 A:GOD802 2.2 38.3 1.0
HC20 A:GOD802 2.5 28.6 1.0
C21 A:GOD802 2.9 29.6 1.0
C20 A:GOD802 3.0 28.6 1.0
O A:HOH953 3.7 64.5 1.0
CD2 A:HIS648 3.7 28.8 1.0
NE2 A:HIS648 3.8 27.8 1.0
CZ A:PHE646 3.9 43.0 1.0
CE1 A:PHE646 4.0 43.1 1.0
C22 A:GOD802 4.2 26.1 1.0
O A:GLY667 4.2 26.7 1.0
C19 A:GOD802 4.3 28.1 1.0
O A:HOH997 4.3 77.5 1.0
C A:GLY667 4.5 28.9 1.0
CD1 A:LEU567 4.5 43.5 1.0
CB A:ASP668 4.6 29.8 1.0
HC22 A:GOD802 4.6 25.4 1.0
HC19 A:GOD802 4.7 27.8 1.0
CG A:HIS648 4.8 27.6 1.0
CA A:GLY667 4.8 24.0 1.0
CE1 A:HIS648 4.9 27.6 1.0
CD1 A:LEU641 4.9 28.8 1.0
CG2 A:ILE666 4.9 25.6 1.0
CE2 A:PHE646 5.0 45.2 1.0

Fluorine binding site 4 out of 5 in 6dki

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Fluorine binding site 4 out of 5 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 19.


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 19. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:31.2
occ:1.00
F29 A:GOD802 0.0 31.2 1.0
C12 A:GOD802 1.4 32.3 1.0
F30 A:GOD802 2.2 30.0 1.0
C14 A:GOD802 2.4 30.2 1.0
C9 A:GOD802 2.5 27.4 1.0
H14B A:GOD802 2.5 30.2 1.0
HC9 A:GOD802 2.6 27.2 1.0
C11 A:GOD802 3.1 26.4 1.0
H11A A:GOD802 3.1 27.3 1.0
N13 A:GOD802 3.2 28.8 1.0
H14A A:GOD802 3.3 30.2 1.0
CG2 A:VAL524 3.4 28.8 1.0
O7 A:GOD802 3.6 27.0 1.0
CD A:LYS544 3.9 46.1 1.0
O A:HOH905 4.0 33.2 1.0
CD1 A:PHE669 4.0 30.9 1.0
CA A:PHE669 4.1 28.2 1.0
H11B A:GOD802 4.2 26.4 1.0
CG1 A:VAL524 4.2 28.3 1.0
O A:PHE669 4.3 36.7 1.0
CG A:LYS544 4.3 31.2 1.0
CB A:LYS544 4.4 23.0 1.0
C15 A:GOD802 4.4 28.1 1.0
HC3 A:GOD802 4.4 25.0 1.0
CG A:PHE669 4.4 29.0 1.0
CB A:VAL524 4.4 28.7 1.0
O A:ASP668 4.5 32.0 1.0
CE1 A:PHE669 4.6 32.1 1.0
H16A A:GOD802 4.6 27.0 1.0
CB A:PHE669 4.6 28.4 1.0
NZ A:LYS544 4.6 62.8 1.0
C A:PHE669 4.6 36.3 1.0
CE A:LYS544 4.7 60.4 1.0
C5 A:GOD802 4.7 25.2 1.0
O A:HOH969 4.7 40.5 1.0

Fluorine binding site 5 out of 5 in 6dki

Go back to Fluorine Binding Sites List in 6dki
Fluorine binding site 5 out of 5 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 19.


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 19. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:30.0
occ:1.00
F30 A:GOD802 0.0 30.0 1.0
C12 A:GOD802 1.4 32.3 1.0
F29 A:GOD802 2.2 31.2 1.0
C14 A:GOD802 2.4 30.2 1.0
C9 A:GOD802 2.4 27.4 1.0
H14A A:GOD802 2.5 30.2 1.0
O7 A:GOD802 2.6 27.0 1.0
H14B A:GOD802 2.9 30.2 1.0
HC9 A:GOD802 2.9 27.2 1.0
CG1 A:VAL524 3.3 28.3 1.0
N13 A:GOD802 3.5 28.8 1.0
C11 A:GOD802 3.6 26.4 1.0
CG2 A:VAL524 3.7 28.8 1.0
C5 A:GOD802 3.8 25.2 1.0
CB A:LYS544 3.8 23.0 1.0
HC3 A:GOD802 4.1 25.0 1.0
CB A:VAL524 4.1 28.7 1.0
CD1 A:PHE589 4.2 27.7 1.0
H11A A:GOD802 4.2 27.3 1.0
H10A A:GOD802 4.3 24.7 1.0
N A:LYS544 4.3 21.2 1.0
CB A:ALA542 4.3 22.5 1.0
CA A:LYS544 4.3 22.3 1.0
C3 A:GOD802 4.4 25.0 1.0
H11B A:GOD802 4.4 26.4 1.0
CG A:LYS544 4.5 31.2 1.0
CE1 A:PHE589 4.5 28.1 1.0
CD A:LYS544 4.6 46.1 1.0
C A:VAL543 4.6 24.0 1.0
C15 A:GOD802 4.8 28.1 1.0
C8 A:GOD802 4.8 24.7 1.0
C A:ALA542 4.8 27.2 1.0
N10 A:GOD802 4.9 25.0 1.0
O A:ALA542 5.0 27.0 1.0
H16B A:GOD802 5.0 28.0 1.0
O A:VAL543 5.0 22.1 1.0
H16A A:GOD802 5.0 27.0 1.0
N A:VAL543 5.0 22.7 1.0
CG A:PHE589 5.0 24.2 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: Sun Dec 13 12:48:05 2020

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