Fluorine in PDB 5m8d: Tubulin MTD265-R1 Complex

The structure of Tubulin MTD265-R1 Complex, PDB code: 5m8d was solved by T.Bohnacker, A.E.Prota, M.O.Steinmetz, M.P.Wymann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.10 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.180, 157.020, 179.980, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21

The structure of Tubulin MTD265-R1 Complex also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Calcium	(Ca)	5 atoms

The binding sites of Fluorine atom in the Tubulin MTD265-R1 Complex (pdb code 5m8d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Tubulin MTD265-R1 Complex, PDB code: 5m8d:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tubulin MTD265-R1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:71.6 occ:0.80 FAZ B:UGI501 0.0 71.6 0.8 CAY B:UGI501 1.3 73.2 0.8 FBA B:UGI501 2.0 85.5 0.8 FBB B:UGI501 2.0 62.3 0.8 CAS B:UGI501 2.2 66.3 0.8 CAR B:UGI501 2.6 64.2 0.8 CG1 B:ILE318 3.4 55.4 1.0 CB B:ALA354 3.4 52.8 1.0 CAH B:UGI501 3.6 59.2 0.8 CB B:CYS241 3.6 57.0 1.0 SG B:CYS241 3.7 76.5 1.0 O B:HOH659 3.7 50.3 1.0 CD1 B:ILE318 3.9 55.4 0.7 CAQ B:UGI501 4.0 73.0 0.8 C4 B:UGI501 4.3 50.5 0.8 C5 B:UGI501 4.6 51.4 0.8 CAO B:UGI501 4.7 68.7 0.8 CB B:ILE318 4.7 52.3 1.0 NAX B:UGI501 4.8 77.8 0.8 CD1 B:LEU248 4.8 0.5 1.0 CA B:ALA354 4.8 56.0 1.0 NAP B:UGI501 4.8 71.6 0.8 CG2 B:ILE318 4.9 52.6 1.0 CB B:ALA316 4.9 38.1 1.0 CD2 B:LEU248 5.0 0.8 1.0

Fluorine binding site 2 out of 3 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tubulin MTD265-R1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:85.5 occ:0.80 FBA B:UGI501 0.0 85.5 0.8 CAY B:UGI501 1.2 73.2 0.8 FBB B:UGI501 2.0 62.3 0.8 FAZ B:UGI501 2.0 71.6 0.8 CAS B:UGI501 2.2 66.3 0.8 CAH B:UGI501 2.9 59.2 0.8 C5 B:UGI501 2.9 51.4 0.8 CAR B:UGI501 3.2 64.2 0.8 C4 B:UGI501 3.2 50.5 0.8 CD1 B:LEU248 3.5 0.5 1.0 CD2 B:LEU248 3.7 0.8 1.0 SG B:CYS241 3.8 76.5 1.0 CD2 B:LEU255 3.9 64.3 1.0 CB B:CYS241 4.0 57.0 1.0 C6 B:UGI501 4.0 57.7 0.8 CG B:LEU248 4.1 0.9 1.0 CAJ B:UGI501 4.1 43.9 0.8 CAO B:UGI501 4.2 68.7 0.8 CB B:ALA250 4.3 72.1 1.0 CB B:ALA354 4.3 52.8 1.0 N3 B:UGI501 4.3 53.4 0.8 CAQ B:UGI501 4.4 73.0 0.8 NAG B:UGI501 4.5 56.7 0.8 NAP B:UGI501 4.8 71.6 0.8 N1 B:UGI501 5.0 56.3 0.8

Fluorine binding site 3 out of 3 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Tubulin MTD265-R1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:62.3 occ:0.80 FBB B:UGI501 0.0 62.3 0.8 CAY B:UGI501 1.2 73.2 0.8 FBA B:UGI501 2.0 85.5 0.8 FAZ B:UGI501 2.0 71.6 0.8 CAS B:UGI501 2.2 66.3 0.8 CAH B:UGI501 2.8 59.2 0.8 C4 B:UGI501 2.9 50.5 0.8 C5 B:UGI501 3.3 51.4 0.8 CAR B:UGI501 3.4 64.2 0.8 N3 B:UGI501 3.5 53.4 0.8 CG B:LYS352 3.7 65.3 1.0 CB B:ALA354 3.8 52.8 1.0 CB B:ALA316 4.0 38.1 1.0 C6 B:UGI501 4.1 57.7 0.8 CAO B:UGI501 4.2 68.7 0.8 CD1 B:LEU248 4.2 0.5 1.0 C2 B:UGI501 4.3 56.9 0.8 CB B:LYS352 4.5 50.8 1.0 CAQ B:UGI501 4.6 73.0 0.8 N1 B:UGI501 4.6 56.3 0.8 CG1 B:ILE318 4.6 55.4 1.0 N B:ALA354 4.7 51.8 1.0 O B:LYS352 4.7 52.4 1.0 CA B:ALA316 4.8 54.7 1.0 CA B:ALA354 4.8 56.0 1.0 NAP B:UGI501 4.9 71.6 0.8 CE B:LYS352 4.9 85.2 1.0 CD B:LYS352 4.9 75.8 1.0 CD1 B:ILE318 5.0 55.4 0.7

T.Bohnacker, A.E.Prota, F.Beaufils, J.E.Burke, A.Melone, A.J.Inglis, D.Rageot, A.M.Sele, V.Cmiljanovic, N.Cmiljanovic, K.Bargsten, A.Aher, A.Akhmanova, J.F.Diaz, D.Fabbro, M.Zvelebil, R.L.Williams, M.O.Steinmetz, M.P.Wymann. Deconvolution of Buparlisib'S Mechanism of Action Defines Specific PI3K and Tubulin Inhibitors For Therapeutic Intervention. Nat Commun V. 8 14683 2017.
ISSN: ESSN 2041-1723
PubMed: 28276440
DOI: 10.1038/NCOMMS14683