Fluorine in PDB 6pmb: Trk-A in Complex with Ligand 1A

All present enzymatic activity of Trk-A in Complex with Ligand 1A:
2.7.10.1;

The structure of Trk-A in Complex with Ligand 1A, PDB code: 6pmb was solved by G.Subramanian, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.17 / 2.81
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	52.109, 52.109, 226.747, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 28.2

The binding sites of Fluorine atom in the Trk-A in Complex with Ligand 1A (pdb code 6pmb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Trk-A in Complex with Ligand 1A, PDB code: 6pmb:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Trk-A in Complex with Ligand 1A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Trk-A in Complex with Ligand 1A within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:25.2 occ:1.00 F1 A:OQM801 0.0 25.2 1.0 C20 A:OQM801 1.3 24.6 1.0 F3 A:OQM801 2.1 25.8 1.0 F2 A:OQM801 2.1 24.5 1.0 C19 A:OQM801 2.4 24.0 1.0 C A:GLY667 3.1 24.1 1.0 C21 A:OQM801 3.1 23.3 1.0 O A:GLY667 3.2 24.2 1.0 C18 A:OQM801 3.3 24.2 1.0 NE2 A:HIS648 3.3 22.9 1.0 CA A:GLY667 3.3 24.3 1.0 CD2 A:HIS648 3.4 24.1 1.0 N A:ASP668 3.7 24.6 1.0 CG2 A:ILE666 3.9 24.2 1.0 N A:GLY667 3.9 24.3 1.0 O A:ILE666 4.0 25.2 1.0 CB A:ASP668 4.0 25.8 1.0 C A:ILE666 4.1 24.8 1.0 CA A:ASP668 4.4 25.3 1.0 C15 A:OQM801 4.4 23.5 1.0 CE1 A:HIS648 4.4 23.2 1.0 C17 A:OQM801 4.4 24.2 1.0 CG A:HIS648 4.6 24.1 1.0 CB A:ILE666 4.8 24.2 1.0 C16 A:OQM801 4.9 23.7 1.0

Fluorine binding site 2 out of 3 in the Trk-A in Complex with Ligand 1A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Trk-A in Complex with Ligand 1A within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:24.5 occ:1.00 F2 A:OQM801 0.0 24.5 1.0 C20 A:OQM801 1.3 24.6 1.0 F3 A:OQM801 2.1 25.8 1.0 F1 A:OQM801 2.1 25.2 1.0 C19 A:OQM801 2.3 24.0 1.0 C18 A:OQM801 2.6 24.2 1.0 CD1 A:LEU567 3.4 41.6 1.0 C21 A:OQM801 3.6 23.3 1.0 CE2 A:PHE646 3.8 32.6 1.0 C17 A:OQM801 4.0 24.2 1.0 CD2 A:HIS648 4.3 24.1 1.0 CZ A:PHE646 4.3 33.3 1.0 CD2 A:PHE646 4.5 34.4 1.0 CD2 A:LEU641 4.6 26.6 1.0 CD1 A:LEU641 4.6 28.2 1.0 NE2 A:HIS648 4.7 22.9 1.0 C15 A:OQM801 4.7 23.5 1.0 C16 A:OQM801 4.8 23.7 1.0 CG A:LEU567 4.8 41.8 1.0 CG2 A:ILE572 5.0 27.6 1.0

Fluorine binding site 3 out of 3 in the Trk-A in Complex with Ligand 1A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Trk-A in Complex with Ligand 1A within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:25.8 occ:1.00 F3 A:OQM801 0.0 25.8 1.0 C20 A:OQM801 1.3 24.6 1.0 F2 A:OQM801 2.1 24.5 1.0 F1 A:OQM801 2.1 25.2 1.0 C19 A:OQM801 2.4 24.0 1.0 C21 A:OQM801 2.9 23.3 1.0 O A:ILE666 3.5 25.2 1.0 C18 A:OQM801 3.5 24.2 1.0 CG2 A:ILE572 3.6 27.6 1.0 CD1 A:LEU567 3.6 41.6 1.0 CA A:GLY667 3.8 24.3 1.0 CG2 A:VAL573 4.1 27.6 1.0 C15 A:OQM801 4.2 23.5 1.0 C A:ILE666 4.2 24.8 1.0 C A:GLY667 4.3 24.1 1.0 N A:GLY667 4.4 24.3 1.0 C17 A:OQM801 4.7 24.2 1.0 CD2 A:LEU564 4.7 34.2 1.0 N A:ASP668 4.8 24.6 1.0 O A:GLY667 4.8 24.2 1.0 CD1 A:ILE572 4.8 28.3 1.0 CB A:ILE572 4.9 27.8 1.0 C16 A:OQM801 4.9 23.7 1.0

G.Subramanian, S.J.Bowen, Y.Zhu, N.Roush, T.Zachary, C.Javens, T.Williams, A.Janssen, A.Gonzales. Synthetic Inhibitor Leads of Human Tropomyosin Receptor Kinase A (Htrka) Rsc Med Chem 2020.
DOI: 10.1039/C9MD00554D