Fluorine in PDB 5njh: Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin

The structure of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin, PDB code: 5njh was solved by A.Sharma, G.S.Calvo, A.E.Prota, J.F.Diaz, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.09 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.430, 158.353, 173.458, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 23.7

The structure of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin (pdb code 5njh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin, PDB code: 5njh:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:51.3 occ:1.00 FAR B:8Z8503 0.0 51.3 1.0 CAO B:8Z8503 1.3 54.2 1.0 CAN B:8Z8503 2.3 50.3 1.0 CAP B:8Z8503 2.3 46.5 1.0 CG B:TYR210 3.5 44.8 1.0 CB B:TYR210 3.5 42.8 1.0 CAM B:8Z8503 3.6 52.9 1.0 CAQ B:8Z8503 3.6 46.9 1.0 CD2 B:TYR210 3.6 47.1 1.0 CG2 B:VAL177 3.6 49.8 1.0 ND2 C:ASN329 3.7 46.6 1.0 CG1 B:VAL177 4.0 49.4 1.0 CAL B:8Z8503 4.0 47.3 1.0 CG C:ASN329 4.0 46.8 1.0 OD1 C:ASN329 4.1 46.8 1.0 CA B:GLU207 4.1 50.0 1.0 CD1 B:TYR210 4.1 44.5 1.0 CB B:VAL177 4.2 48.8 1.0 O B:HOH653 4.3 62.4 1.0 CE2 B:TYR210 4.3 49.1 1.0 CG B:GLU207 4.6 53.0 1.0 O B:ASN206 4.6 51.1 1.0 FAS B:8Z8503 4.6 49.4 1.0 FAT B:8Z8503 4.6 51.5 1.0 CB B:GLU207 4.7 50.5 1.0 O B:GLU207 4.7 54.9 1.0 CE1 B:TYR210 4.8 46.4 1.0 CZ B:TYR210 4.8 48.6 1.0 N B:GLU207 4.8 46.4 1.0 C B:GLU207 4.9 52.4 1.0

Fluorine binding site 2 out of 3 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:49.4 occ:1.00 FAS B:8Z8503 0.0 49.4 1.0 CAM B:8Z8503 1.3 52.9 1.0 CAN B:8Z8503 2.3 50.3 1.0 CAL B:8Z8503 2.4 47.3 1.0 CAA B:8Z8503 2.8 51.0 1.0 CE1 B:TYR224 3.3 50.4 1.0 CAF B:8Z8503 3.4 54.0 1.0 CAB B:8Z8503 3.5 52.8 1.0 CAO B:8Z8503 3.6 54.2 1.0 CAQ B:8Z8503 3.6 46.9 1.0 CD2 B:LEU227 3.7 41.9 1.0 OH B:TYR224 3.8 50.8 1.0 CL1 B:8Z8503 3.8 56.9 1.0 NAH B:8Z8503 3.8 58.4 1.0 CZ B:TYR224 3.9 50.1 1.0 CAP B:8Z8503 4.1 46.5 1.0 CD1 B:TYR224 4.1 50.2 1.0 CB B:ASN206 4.2 44.4 1.0 CAV B:8Z8503 4.3 48.2 1.0 ND2 B:ASN206 4.4 41.2 1.0 CAU B:8Z8503 4.4 56.8 1.0 NAE B:8Z8503 4.4 52.5 1.0 NAC B:8Z8503 4.5 54.5 1.0 CG B:ASN206 4.5 42.5 1.0 CAJ B:8Z8503 4.6 55.9 1.0 CAK B:8Z8503 4.6 59.5 1.0 FAR B:8Z8503 4.6 51.3 1.0 FAT B:8Z8503 4.7 51.5 1.0 CAI B:8Z8503 4.8 62.5 1.0 CAD B:8Z8503 4.8 54.1 1.0 O B:ASN206 4.8 51.1 1.0

Fluorine binding site 3 out of 3 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:51.5 occ:1.00 FAT B:8Z8503 0.0 51.5 1.0 CAQ B:8Z8503 1.3 46.9 1.0 CAP B:8Z8503 2.3 46.5 1.0 CAL B:8Z8503 2.3 47.3 1.0 CAA B:8Z8503 2.8 51.0 1.0 O C:PRO325 3.3 51.1 1.0 C C:PRO325 3.4 51.2 1.0 CAU B:8Z8503 3.4 56.8 1.0 CAF B:8Z8503 3.4 54.0 1.0 CAB B:8Z8503 3.5 52.8 1.0 CAO B:8Z8503 3.6 54.2 1.0 N C:LYS326 3.6 57.7 1.0 CAM B:8Z8503 3.6 52.9 1.0 CE1 B:TYR210 3.6 46.4 1.0 CB C:ASN329 3.7 46.7 1.0 CL1 B:8Z8503 3.7 56.9 1.0 CA C:LYS326 3.8 57.3 1.0 CB C:PRO325 3.8 52.1 1.0 NAH B:8Z8503 3.9 58.4 1.0 CD1 B:TYR210 4.0 44.5 1.0 CAN B:8Z8503 4.1 50.3 1.0 CA C:PRO325 4.2 51.7 1.0 CAV B:8Z8503 4.2 48.2 1.0 CZ B:TYR210 4.3 48.6 1.0 CG C:ASN329 4.4 46.8 1.0 NAE B:8Z8503 4.4 52.5 1.0 CAZ B:8Z8503 4.4 48.3 1.0 NAC B:8Z8503 4.5 54.5 1.0 OH B:TYR210 4.6 50.6 1.0 FAR B:8Z8503 4.6 51.3 1.0 CB C:LYS326 4.7 58.0 1.0 FAS B:8Z8503 4.7 49.4 1.0 ND2 C:ASN329 4.7 46.6 1.0 O B:PRO222 4.8 51.7 1.0 C C:LYS326 4.8 57.3 1.0 CAD B:8Z8503 4.8 54.1 1.0 CG B:TYR210 4.9 44.8 1.0 OD1 C:ASN329 5.0 46.8 1.0 CA C:ASN329 5.0 46.1 1.0

G.Saez-Calvo, A.Sharma, F.A.Balaguer, I.Barasoain, J.Rodriguez-Salarichs, N.Olieric, H.Munoz-Hernandez, M.A.Berbis, S.Wendeborn, M.A.Penalva, R.Matesanz, A.Canales, A.E.Prota, J.Jimenez-Barbero, J.M.Andreu, C.Lamberth, M.O.Steinmetz, J.F.Diaz. Triazolopyrimidines Are Microtubule-Stabilizing Agents That Bind the Vinca Inhibitor Site of Tubulin. Cell Chem Biol V. 24 737 2017.
ISSN: ESSN 2451-9456
PubMed: 28579361
DOI: 10.1016/J.CHEMBIOL.2017.05.016