Fluorine in PDB 5sb7: Tubulin-Todalam-18-Complex

The structure of Tubulin-Todalam-18-Complex, PDB code: 5sb7 was solved by T.Muehlethaler, L.Milanos, J.A.Ortega, T.B.Blum, D.Gioia, 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)	48.08 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.148, 158.288, 179.988, 90, 90, 90
R / Rfree (%)	20.2 / 23.5

The structure of Tubulin-Todalam-18-Complex also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Tubulin-Todalam-18-Complex (pdb code 5sb7). 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-18-Complex, PDB code: 5sb7:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Tubulin-Todalam-18-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-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F504 b:66.7 occ:0.90 F1 C:4I2504 0.0 66.7 0.9 C7 C:4I2504 1.4 62.3 0.9 F2 C:4I2504 2.2 68.3 0.9 F3 C:4I2504 2.2 66.2 0.9 C4 C:4I2504 2.3 55.5 0.9 C3 C:4I2504 2.8 43.1 0.9 CG C:LEU136 3.0 45.1 1.0 CD1 C:LEU136 3.1 46.8 1.0 SG C:CYS4 3.1 40.0 0.4 CD2 C:LEU136 3.2 52.9 1.0 C5 C:4I2504 3.5 57.2 0.9 SG C:CYS4 3.9 42.0 0.6 CZ C:PHE52 3.9 34.7 1.0 CB C:CYS4 4.1 34.3 0.6 CB C:CYS4 4.1 34.3 0.4 C2 C:4I2504 4.1 50.1 0.9 CG2 C:THR239 4.5 35.2 1.0 CD1 C:LEU242 4.5 56.2 1.0 CB C:LEU136 4.5 31.1 1.0 CE1 C:PHE52 4.6 36.7 1.0 C6 C:4I2504 4.7 58.6 0.9 CE2 C:PHE52 4.9 40.5 1.0 CD1 C:LEU252 4.9 47.3 0.2 C1 C:4I2504 4.9 56.9 0.9

Fluorine binding site 2 out of 3 in the Tubulin-Todalam-18-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-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F504 b:68.3 occ:0.90 F2 C:4I2504 0.0 68.3 0.9 C7 C:4I2504 1.4 62.3 0.9 F1 C:4I2504 2.2 66.7 0.9 F3 C:4I2504 2.2 66.2 0.9 C4 C:4I2504 2.3 55.5 0.9 C5 C:4I2504 2.7 57.2 0.9 CD1 C:LEU252 3.0 47.3 0.2 CD1 C:LEU242 3.1 56.2 1.0 C3 C:4I2504 3.6 43.1 0.9 CD2 C:LEU242 4.0 63.0 1.0 CG C:LEU252 4.0 49.7 0.8 C6 C:4I2504 4.1 58.6 0.9 CG C:LEU242 4.1 58.9 1.0 CB C:LEU252 4.1 47.7 0.8 CD1 C:LEU252 4.2 51.3 0.8 CB C:LEU252 4.2 47.8 0.2 CG C:LEU252 4.2 49.0 0.2 CD2 C:LEU136 4.5 52.9 1.0 CD2 C:LEU167 4.6 47.6 1.0 C2 C:4I2504 4.7 50.1 0.9 SG C:CYS4 4.7 42.0 0.6 CG2 C:THR239 4.8 35.2 1.0 CD1 C:LEU136 4.9 46.8 1.0 C1 C:4I2504 4.9 56.9 0.9 N1 C:4I2504 4.9 55.6 0.9 CG C:LEU136 4.9 45.1 1.0

Fluorine binding site 3 out of 3 in the Tubulin-Todalam-18-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-18-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F504 b:66.2 occ:0.90 F3 C:4I2504 0.0 66.2 0.9 C7 C:4I2504 1.4 62.3 0.9 F1 C:4I2504 2.2 66.7 0.9 F2 C:4I2504 2.2 68.3 0.9 C4 C:4I2504 2.3 55.5 0.9 SG C:CYS4 2.5 42.0 0.6 CD2 C:LEU242 3.1 63.0 1.0 C3 C:4I2504 3.1 43.1 0.9 CD1 C:LEU242 3.2 56.2 1.0 C5 C:4I2504 3.3 57.2 0.9 CG C:LEU242 3.6 58.9 1.0 CB C:CYS4 3.7 34.3 0.6 CB C:CYS4 3.7 34.3 0.4 SG C:CYS4 3.8 40.0 0.4 CE1 C:PHE52 4.1 36.7 1.0 CB C:LEU242 4.1 49.0 1.0 CZ C:PHE52 4.1 34.7 1.0 OE1 C:GLN133 4.1 61.4 1.0 C2 C:4I2504 4.3 50.1 0.9 C6 C:4I2504 4.5 58.6 0.9 C1 C:4I2504 4.9 56.9 0.9

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