Fluorine in PDB 6pma: Trk-A in Complex with Ligand

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

The structure of Trk-A in Complex with Ligand, PDB code: 6pma 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)	45.16 / 2.53
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	52.094, 52.094, 227.160, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 26.6

The structure of Trk-A in Complex with Ligand also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Trk-A in Complex with Ligand (pdb code 6pma). 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, PDB code: 6pma:
Jump to Fluorine binding site number: 1; 2; 3;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:47.2 occ:1.00 F1 A:OQS801 0.0 47.2 1.0 C14 A:OQS801 1.3 44.0 1.0 F2 A:OQS801 2.0 43.0 1.0 F3 A:OQS801 2.1 48.4 1.0 C13 A:OQS801 2.3 41.7 1.0 C12 A:OQS801 2.7 42.6 1.0 CG2 A:ILE572 3.5 35.5 1.0 C15 A:OQS801 3.5 43.6 1.0 O A:ILE666 3.6 36.1 1.0 CA A:GLY667 4.1 32.7 1.0 C11 A:OQS801 4.1 42.7 1.0 CD1 A:LEU567 4.2 60.0 1.0 CD1 A:ILE572 4.3 42.9 1.0 C A:ILE666 4.3 32.6 1.0 CD2 A:LEU564 4.4 44.0 1.0 C A:GLY667 4.5 33.6 1.0 N A:GLY667 4.5 31.4 1.0 CG1 A:VAL573 4.6 45.0 1.0 C16 A:OQS801 4.7 43.7 1.0 CB A:ILE572 4.8 37.2 1.0 N A:ASP668 4.8 34.0 1.0 O3 A:OQS801 4.9 38.8 1.0 C17 A:OQS801 4.9 45.1 1.0 O A:GLY667 4.9 29.6 1.0 N4 A:OQS801 5.0 42.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:43.0 occ:1.00 F2 A:OQS801 0.0 43.0 1.0 C14 A:OQS801 1.3 44.0 1.0 F3 A:OQS801 2.0 48.4 1.0 F1 A:OQS801 2.0 47.2 1.0 C13 A:OQS801 2.3 41.7 1.0 C15 A:OQS801 2.8 43.6 1.0 C12 A:OQS801 3.5 42.6 1.0 CD1 A:LEU567 3.5 60.0 1.0 CD1 A:LEU641 3.7 46.6 1.0 CE1 A:PHE646 3.8 37.7 1.0 CD2 A:LEU641 4.1 44.7 1.0 C16 A:OQS801 4.1 43.7 1.0 CZ A:PHE646 4.3 35.7 1.0 CD1 A:PHE646 4.5 39.7 1.0 CD2 A:HIS648 4.5 30.6 1.0 CG A:LEU641 4.6 45.5 1.0 C11 A:OQS801 4.7 42.7 1.0 CD1 A:ILE572 4.7 42.9 1.0 CG A:LEU567 4.8 60.4 1.0 C17 A:OQS801 4.9 45.1 1.0 CG2 A:ILE572 4.9 35.5 1.0 NE2 A:HIS648 4.9 28.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:48.4 occ:1.00 F3 A:OQS801 0.0 48.4 1.0 C14 A:OQS801 1.3 44.0 1.0 F2 A:OQS801 2.0 43.0 1.0 F1 A:OQS801 2.1 47.2 1.0 C13 A:OQS801 2.3 41.7 1.0 C15 A:OQS801 3.1 43.6 1.0 C12 A:OQS801 3.1 42.6 1.0 NE2 A:HIS648 3.4 28.0 1.0 O A:GLY667 3.4 29.6 1.0 CD2 A:HIS648 3.4 30.6 1.0 C A:GLY667 3.4 33.6 1.0 CA A:GLY667 3.7 32.7 1.0 CG2 A:ILE666 3.8 33.7 1.0 N A:ASP668 3.9 34.0 1.0 N A:GLY667 4.0 31.4 1.0 O A:ILE666 4.1 36.1 1.0 C A:ILE666 4.2 32.6 1.0 CB A:ASP668 4.2 42.4 1.0 C16 A:OQS801 4.3 43.7 1.0 C11 A:OQS801 4.4 42.7 1.0 CD1 A:LEU641 4.4 46.6 1.0 CE1 A:HIS648 4.5 30.3 1.0 CG A:HIS648 4.5 30.4 1.0 CB A:ILE666 4.7 31.6 1.0 CA A:ASP668 4.7 38.8 1.0 C17 A:OQS801 4.8 45.1 1.0 CD1 A:ILE572 5.0 42.9 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