Fluorine in PDB 3wze: Kdr in Complex with Ligand Sorafenib

All present enzymatic activity of Kdr in Complex with Ligand Sorafenib:
2.7.10.1;

The structure of Kdr in Complex with Ligand Sorafenib, PDB code: 3wze was solved by K.Okamoto, M.Ikemori_Kawada, A.Inoue, J.Matsui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.78 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.921, 57.357, 52.170, 90.00, 94.17, 90.00
R / Rfree (%)	18.5 / 22.4

The structure of Kdr in Complex with Ligand Sorafenib also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

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

Fluorine binding site 1 out of 3 in the Kdr in Complex with Ligand Sorafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Kdr in Complex with Ligand Sorafenib within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:39.6 occ:1.00 F8 A:BAX1201 0.0 39.6 1.0 C7 A:BAX1201 1.3 36.9 1.0 F9 A:BAX1201 2.1 37.8 1.0 F10 A:BAX1201 2.1 36.4 1.0 C6 A:BAX1201 2.3 27.5 1.0 C5 A:BAX1201 3.0 33.5 1.0 CL11 A:BAX1201 3.1 51.0 1.0 CD2 A:HIS1026 3.2 30.0 1.0 C1 A:BAX1201 3.4 31.6 1.0 NE2 A:HIS1026 3.4 35.3 1.0 CG2 A:ILE1044 3.6 36.7 1.0 CD1 A:LEU1019 3.9 53.9 1.0 C A:CYS1045 4.1 26.7 1.0 O A:CYS1045 4.1 28.5 1.0 CA A:CYS1045 4.2 23.8 1.0 CG A:HIS1026 4.3 34.4 1.0 N A:CYS1045 4.3 28.3 1.0 C4 A:BAX1201 4.3 35.5 1.0 C A:ILE1044 4.5 28.0 1.0 CE1 A:HIS1026 4.5 37.1 1.0 N A:ASP1046 4.5 27.3 1.0 O A:ILE1044 4.5 31.7 1.0 C2 A:BAX1201 4.6 31.5 1.0 CB A:ILE1044 4.6 29.0 1.0 CB A:ASP1046 4.6 31.8 1.0 CD2 A:LEU1019 4.7 62.8 1.0 CG A:LEU1019 4.9 44.1 1.0 ND1 A:HIS1026 4.9 36.9 1.0 C3 A:BAX1201 4.9 37.9 1.0

Fluorine binding site 2 out of 3 in the Kdr in Complex with Ligand Sorafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Kdr in Complex with Ligand Sorafenib within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:37.8 occ:1.00 F9 A:BAX1201 0.0 37.8 1.0 C7 A:BAX1201 1.3 36.9 1.0 F10 A:BAX1201 2.0 36.4 1.0 F8 A:BAX1201 2.1 39.6 1.0 C6 A:BAX1201 2.3 27.5 1.0 C1 A:BAX1201 2.7 31.6 1.0 O A:ILE1044 3.1 31.7 1.0 CA A:CYS1045 3.5 23.8 1.0 C A:ILE1044 3.6 28.0 1.0 CG1 A:VAL898 3.7 34.1 1.0 C5 A:BAX1201 3.7 33.5 1.0 N A:CYS1045 3.8 28.3 1.0 CG1 A:VAL899 4.0 31.3 1.0 C A:CYS1045 4.1 26.7 1.0 CG2 A:ILE1044 4.1 36.7 1.0 C2 A:BAX1201 4.1 31.5 1.0 O15 A:BAX1201 4.3 28.5 1.0 CL11 A:BAX1201 4.4 51.0 1.0 CB A:ILE1044 4.5 29.0 1.0 N A:ASP1046 4.5 27.3 1.0 N A:VAL899 4.5 27.4 1.0 CD2 A:LEU889 4.6 34.5 1.0 O A:CYS1045 4.6 28.5 1.0 CA A:ILE1044 4.7 27.3 1.0 CB A:CYS1045 4.7 30.0 1.0 CB A:VAL898 4.8 33.2 1.0 C4 A:BAX1201 4.8 35.5 1.0 C3 A:BAX1201 4.9 37.9 1.0 CA A:VAL898 4.9 32.0 1.0 N12 A:BAX1201 5.0 26.3 1.0

Fluorine binding site 3 out of 3 in the Kdr in Complex with Ligand Sorafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Kdr in Complex with Ligand Sorafenib within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:36.4 occ:1.00 F10 A:BAX1201 0.0 36.4 1.0 C7 A:BAX1201 1.3 36.9 1.0 F9 A:BAX1201 2.0 37.8 1.0 F8 A:BAX1201 2.1 39.6 1.0 C6 A:BAX1201 2.3 27.5 1.0 C5 A:BAX1201 2.9 33.5 1.0 CL11 A:BAX1201 3.0 51.0 1.0 C1 A:BAX1201 3.4 31.6 1.0 CD1 A:ILE892 3.7 41.9 1.0 CD2 A:LEU1019 3.7 62.8 1.0 CG1 A:VAL898 3.8 34.1 1.0 CD1 A:LEU1019 4.0 53.9 1.0 CG A:LEU1019 4.2 44.1 1.0 C4 A:BAX1201 4.3 35.5 1.0 CD2 A:LEU889 4.4 34.5 1.0 C2 A:BAX1201 4.6 31.5 1.0 C3 A:BAX1201 4.9 37.9 1.0 CG1 A:ILE892 4.9 36.9 1.0 CG2 A:ILE1044 4.9 36.7 1.0 O A:ILE1044 5.0 31.7 1.0

K.Okamoto, M.Ikemori-Kawada, A.Jestel, K.Von Konig, Y.Funahashi, T.Matsushima, A.Tsuruoka, A.Inoue, J.Matsui. Distinct Binding Mode of Multikinase Inhibitor Lenvatinib Revealed By Biochemical Characterization. Acs Med.Chem.Lett. V. 6 89 2015.
ISSN: ISSN 1948-5875
PubMed: 25589937
DOI: 10.1021/ML500394M