Fluorine in PDB 6dkb: Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.

All present enzymatic activity of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.:
2.7.10.1;

The structure of Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B., PDB code: 6dkb 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)	41.00 / 2.68
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.490, 45.970, 79.270, 90.00, 126.97, 90.00
R / Rfree (%)	21.6 / 24.5

The binding sites of Fluorine atom in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B. (pdb code 6dkb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B., PDB code: 6dkb:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.


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 10B. within 5.0Å range: probe atom residue distance (Å) B Occ A:F4000 b:81.8 occ:1.00 F31 A:FKY4000 0.0 81.8 1.0 C30 A:FKY4000 1.3 78.7 1.0 F33 A:FKY4000 2.1 76.9 1.0 F32 A:FKY4000 2.1 80.3 1.0 O29 A:FKY4000 2.2 73.4 1.0 C26 A:FKY4000 2.7 69.2 1.0 O A:ILE666 2.9 55.6 1.0 C25 A:FKY4000 3.2 69.4 1.0 C A:ILE666 3.3 55.1 1.0 CA A:GLY667 3.6 51.3 1.0 N A:GLY667 3.6 51.7 1.0 C27 A:FKY4000 3.7 66.2 1.0 CG2 A:ILE666 3.7 54.4 1.0 O A:GLY667 3.7 54.1 1.0 C A:GLY667 3.8 55.6 1.0 CB A:ILE666 4.0 53.1 1.0 CD1 A:ILE572 4.2 59.2 1.0 CD2 A:HIS648 4.2 64.8 1.0 CG2 A:ILE572 4.2 57.8 1.0 NE2 A:HIS648 4.2 64.4 1.0 CA A:ILE666 4.3 50.2 1.0 C24 A:FKY4000 4.4 68.2 1.0 C28 A:FKY4000 4.7 65.0 1.0 N A:ASP668 4.8 53.4 1.0 CD1 A:LEU641 4.9 59.5 1.0 CB A:ILE572 5.0 57.8 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.


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 10B. within 5.0Å range: probe atom residue distance (Å) B Occ A:F4000 b:80.3 occ:1.00 F32 A:FKY4000 0.0 80.3 1.0 C30 A:FKY4000 1.3 78.7 1.0 F33 A:FKY4000 2.1 76.9 1.0 O29 A:FKY4000 2.1 73.4 1.0 F31 A:FKY4000 2.1 81.8 1.0 C26 A:FKY4000 3.4 69.2 1.0 CD2 A:LEU641 3.6 58.5 1.0 CD1 A:LEU641 3.8 59.5 1.0 CE1 A:PHE646 3.9 74.0 1.0 CD1 A:LEU567 4.0 73.1 1.0 CD2 A:HIS648 4.2 64.8 1.0 CD1 A:ILE572 4.2 59.2 1.0 CZ A:PHE646 4.2 73.1 1.0 CG A:LEU641 4.3 60.7 1.0 C25 A:FKY4000 4.3 69.4 1.0 C27 A:FKY4000 4.3 66.2 1.0 CG2 A:ILE572 4.4 57.8 1.0 CD1 A:PHE646 4.6 74.0 1.0 NE2 A:HIS648 4.8 64.4 1.0 O A:ILE666 4.9 55.6 1.0 CG A:LEU567 5.0 73.0 1.0 CG2 A:ILE666 5.0 54.4 1.0 CD2 A:LEU567 5.0 73.0 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.


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 10B. within 5.0Å range: probe atom residue distance (Å) B Occ A:F4000 b:76.9 occ:1.00 F33 A:FKY4000 0.0 76.9 1.0 C30 A:FKY4000 1.3 78.7 1.0 F32 A:FKY4000 2.1 80.3 1.0 F31 A:FKY4000 2.1 81.8 1.0 O29 A:FKY4000 2.2 73.4 1.0 C26 A:FKY4000 2.8 69.2 1.0 C27 A:FKY4000 3.1 66.2 1.0 CD2 A:HIS648 3.2 64.8 1.0 NE2 A:HIS648 3.2 64.4 1.0 O A:GLY667 3.8 54.1 1.0 C25 A:FKY4000 4.0 69.4 1.0 C A:GLY667 4.1 55.6 1.0 CB A:ASP668 4.1 55.9 1.0 C28 A:FKY4000 4.3 65.0 1.0 CG A:HIS648 4.3 64.2 1.0 CE1 A:PHE646 4.3 74.0 1.0 CE1 A:HIS648 4.4 64.0 1.0 CZ A:PHE646 4.5 73.1 1.0 CA A:GLY667 4.6 51.3 1.0 N A:ASP668 4.7 53.4 1.0 CG2 A:ILE666 4.8 54.4 1.0 CD1 A:LEU641 4.9 59.5 1.0 O A:ILE666 4.9 55.6 1.0 OD2 A:ASP668 4.9 87.6 1.0 N A:GLY667 5.0 51.7 1.0 ND1 A:HIS648 5.0 65.2 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Trk-A in Complex with the Pan-Trk Kinase Inhibitor, Compound 10B.


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 10B. within 5.0Å range: probe atom residue distance (Å) B Occ A:F4000 b:61.9 occ:1.00 F34 A:FKY4000 0.0 61.9 1.0 C15 A:FKY4000 1.4 61.2 1.0 C14 A:FKY4000 2.4 61.7 1.0 C16 A:FKY4000 2.4 61.9 1.0 O13 A:FKY4000 2.7 61.9 1.0 N17 A:FKY4000 2.9 65.7 1.0 C19 A:FKY4000 3.0 63.6 1.0 CG A:PHE589 3.3 55.3 1.0 CB A:PHE589 3.5 55.3 1.0 N36 A:FKY4000 3.5 68.6 1.0 C20 A:FKY4000 3.5 67.3 1.0 C18 A:FKY4000 3.5 64.1 1.0 CD1 A:PHE589 3.6 56.9 1.0 CD2 A:PHE589 3.8 56.0 1.0 C22 A:FKY4000 3.9 65.9 1.0 C10 A:FKY4000 4.0 63.4 1.0 O21 A:FKY4000 4.3 67.9 1.0 CE1 A:PHE589 4.3 56.8 1.0 C35 A:FKY4000 4.4 68.7 1.0 CG2 A:VAL573 4.4 61.7 1.0 CE2 A:PHE589 4.4 58.3 1.0 CB A:ALA542 4.4 56.6 1.0 CD1 A:LEU657 4.5 57.4 1.0 CZ A:PHE589 4.6 56.2 1.0 C9 A:FKY4000 4.6 65.5 1.0 N11 A:FKY4000 4.9 62.8 1.0 CG1 A:VAL573 4.9 61.8 1.0 CA A:PHE589 5.0 54.3 1.0

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