Fluorine in PDB 7z7d: Tubulin-Todalam-Vinblastine-Complex

The structure of Tubulin-Todalam-Vinblastine-Complex, PDB code: 7z7d was solved by T.Muehlethaler, L.Milanos, J.A.Ortega, T.B.Blum, D.Gioia, B.Roy, A.E.Prota, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.60 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.286, 157.296, 182.526, 90, 90, 90
R / Rfree (%)	20.4 / 23.6

The structure of Tubulin-Todalam-Vinblastine-Complex also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Magnesium	(Mg)	5 atoms

The binding sites of Fluorine atom in the Tubulin-Todalam-Vinblastine-Complex (pdb code 7z7d). 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-Todalam-Vinblastine-Complex, PDB code: 7z7d:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Tubulin-Todalam-Vinblastine-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F504 b:60.4 occ:0.30 F1 C:4I2504 0.0 60.4 0.3 C7 C:4I2504 1.4 69.4 0.7 F3 C:4I2504 2.2 54.7 0.3 F2 C:4I2504 2.2 58.3 0.3 C4 C:4I2504 2.4 52.0 0.7 C3 C:4I2504 2.8 52.7 0.7 CD2 C:LEU136 3.0 48.4 1.0 CD1 C:LEU136 3.2 50.0 1.0 CG C:LEU136 3.5 52.6 1.0 C5 C:4I2504 3.6 48.4 0.7 CG2 C:THR239 4.0 33.2 1.0 C2 C:4I2504 4.2 31.6 0.7 CD2 C:LEU167 4.4 53.6 1.0 CG2 C:ILE238 4.5 36.3 1.0 SG C:CYS4 4.6 45.1 0.5 CD1 C:LEU242 4.6 67.5 1.0 CD2 C:LEU252 4.7 80.7 1.0 C6 C:4I2504 4.7 56.0 0.7 C1 C:4I2504 5.0 45.2 0.7

Fluorine binding site 2 out of 3 in the Tubulin-Todalam-Vinblastine-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F504 b:58.3 occ:0.30 F2 C:4I2504 0.0 58.3 0.3 C7 C:4I2504 1.4 69.4 0.7 F3 C:4I2504 2.2 54.7 0.3 F1 C:4I2504 2.2 60.4 0.3 C4 C:4I2504 2.3 52.0 0.7 C5 C:4I2504 2.7 48.4 0.7 CG C:LEU252 3.3 70.0 1.0 CD2 C:LEU252 3.3 80.7 1.0 CD2 C:LEU167 3.5 53.6 1.0 C3 C:4I2504 3.6 52.7 0.7 CD1 C:LEU252 3.7 74.7 1.0 CG2 C:ILE238 4.0 36.3 1.0 C6 C:4I2504 4.1 56.0 0.7 CD2 C:LEU136 4.5 48.4 1.0 OE1 C:GLN256 4.5 25.9 0.3 CB C:LEU252 4.7 60.0 1.0 C2 C:4I2504 4.8 31.6 0.7 CG C:LEU167 4.8 51.2 1.0 N1 C:4I2504 4.9 48.0 0.7 O C:ILE238 4.9 41.9 1.0 C1 C:4I2504 4.9 45.2 0.7

Fluorine binding site 3 out of 3 in the Tubulin-Todalam-Vinblastine-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F504 b:54.7 occ:0.30 F3 C:4I2504 0.0 54.7 0.3 C7 C:4I2504 1.4 69.4 0.7 F1 C:4I2504 2.2 60.4 0.3 F2 C:4I2504 2.2 58.3 0.3 C4 C:4I2504 2.3 52.0 0.7 CD1 C:LEU242 3.0 67.5 1.0 CD2 C:LEU252 3.0 80.7 1.0 C3 C:4I2504 3.1 52.7 0.7 C5 C:4I2504 3.2 48.4 0.7 CG C:LEU252 3.5 70.0 1.0 CG C:LEU242 3.8 58.9 1.0 C2 C:4I2504 4.3 31.6 0.7 C6 C:4I2504 4.5 56.0 0.7 CB C:LEU252 4.5 60.0 1.0 CD2 C:LEU242 4.5 64.6 1.0 CD1 C:LEU252 4.6 74.7 1.0 CG2 C:THR239 4.7 33.2 1.0 O C:ILE238 4.7 41.9 1.0 SG C:CYS4 4.7 34.5 0.5 CA C:THR239 4.9 31.4 1.0 C1 C:4I2504 4.9 45.2 0.7 CB C:LEU242 5.0 43.7 1.0

T.Muhlethaler, L.Milanos, J.A.Ortega, T.B.Blum, D.Gioia, B.Roy, A.E.Prota, A.Cavalli, M.O.Steinmetz. Rational Design of A Novel Tubulin Inhibitor with A Unique Mechanism of Action. Angew.Chem.Int.Ed.Engl. V. 61 04052 2022.
ISSN: ESSN 1521-3773
PubMed: 35404502
DOI: 10.1002/ANIE.202204052