Fluorine in PDB 6xet: Tubulin-RB3_SLD in Complex with Compound 60C

The structure of Tubulin-RB3_SLD in Complex with Compound 60C, PDB code: 6xet was solved by S.W.White, M.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.46 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.097, 126.938, 250.461, 90, 90, 90
R / Rfree (%)	16.8 / 23.1

The structure of Tubulin-RB3_SLD in Complex with Compound 60C also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Tubulin-RB3_SLD in Complex with Compound 60C (pdb code 6xet). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Tubulin-RB3_SLD in Complex with Compound 60C, PDB code: 6xet:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Tubulin-RB3_SLD in Complex with Compound 60C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tubulin-RB3_SLD in Complex with Compound 60C within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:66.7 occ:1.00 F29 B:TU2502 0.0 66.7 1.0 C28 B:TU2502 1.4 58.1 1.0 C27 B:TU2502 2.4 51.2 1.0 C15 B:TU2502 2.4 58.4 1.0 O01 B:TU2502 2.9 63.0 1.0 C02 B:TU2502 2.9 63.8 1.0 CA B:ALA248 3.5 53.0 1.0 O B:LEU246 3.5 61.1 1.0 CD B:LYS252 3.6 57.3 1.0 CG B:LEU246 3.6 71.7 1.0 N16 B:TU2502 3.6 59.5 1.0 C26 B:TU2502 3.6 56.4 1.0 CB B:LYS252 3.7 48.3 1.0 CB B:ALA248 4.0 56.5 1.0 N B:ALA248 4.1 66.7 1.0 C17 B:TU2502 4.1 61.8 1.0 CD1 B:LEU246 4.1 75.5 1.0 CG B:LYS252 4.2 50.6 1.0 C03 B:TU2502 4.2 63.2 1.0 O B:ASN247 4.2 74.9 1.0 N B:ASP249 4.3 42.0 1.0 NZ B:LYS252 4.3 59.8 1.0 C B:LEU246 4.3 60.1 1.0 C B:ASN247 4.3 73.5 1.0 CB B:LEU246 4.4 70.0 1.0 CE B:LYS252 4.4 64.4 1.0 C B:ALA248 4.4 46.0 1.0 CD2 B:LEU246 4.5 77.2 1.0 C14 B:TU2502 4.8 58.8 1.0 CA B:LEU246 4.8 70.6 1.0 CA B:LYS252 5.0 49.1 1.0

Fluorine binding site 2 out of 2 in the Tubulin-RB3_SLD in Complex with Compound 60C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tubulin-RB3_SLD in Complex with Compound 60C within 5.0Å range: probe atom residue distance (Å) B Occ D:F502 b:51.5 occ:1.00 F29 D:TU2502 0.0 51.5 1.0 C28 D:TU2502 1.4 47.0 1.0 C15 D:TU2502 2.4 46.7 1.0 C27 D:TU2502 2.4 39.4 1.0 O01 D:TU2502 2.8 48.7 1.0 C02 D:TU2502 2.8 48.9 1.0 CD D:LYS252 3.2 56.9 1.0 CA D:ALA248 3.4 45.1 1.0 CB D:LYS252 3.4 47.5 1.0 N16 D:TU2502 3.6 47.8 1.0 O D:LEU246 3.6 59.5 1.0 C26 D:TU2502 3.7 41.6 1.0 CG D:LEU246 3.8 59.6 1.0 CB D:ALA248 3.8 45.2 1.0 CG D:LYS252 3.9 50.3 1.0 N D:ALA248 4.1 52.5 1.0 C17 D:TU2502 4.1 49.0 1.0 C03 D:TU2502 4.1 51.3 1.0 O D:ASN247 4.2 58.2 1.0 N D:ASP249 4.2 33.3 1.0 CD1 D:LEU246 4.3 61.2 1.0 C D:ALA248 4.3 38.6 1.0 C D:ASN247 4.4 57.0 1.0 CD2 D:LEU246 4.4 57.3 1.0 CE D:LYS252 4.4 68.2 1.0 NZ D:LYS252 4.5 72.1 1.0 C D:LEU246 4.6 55.7 1.0 C14 D:TU2502 4.7 52.4 1.0 CA D:LYS252 4.7 49.1 1.0 C D:LYS252 4.8 46.6 1.0 CB D:LEU246 4.8 60.2 1.0 N D:LEU253 5.0 45.5 1.0

H.Chen, S.Deng, N.Albadari, M.K.Yun, S.Zhang, Y.Li, D.Ma, D.N.Parke, L.Yang, T.N.Seagroves, S.W.White, D.D.Miller, W.Li. Design, Synthesis, and Biological Evaluation of Stable Colchicine-Binding Site Tubulin Inhibitors 6-Aryl-2-Benzoyl-Pyridines As Potential Anticancer Agents. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34378386
DOI: 10.1021/ACS.JMEDCHEM.1C00715