Chlorine in PDB 6brf: Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B, PDB code: 6brf was solved by G.Kumar, Y.Wang, W.Li, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.78 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.129, 157.747, 181.596, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.7

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Calcium	(Ca)	2 atoms

The binding sites of Chlorine atom in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B (pdb code 6brf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B, PDB code: 6brf:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl505 b:44.3 occ:1.00 CL1 B:E44505 0.0 44.3 1.0 C1 B:E44505 1.7 40.0 1.0 N4 B:E44505 2.6 39.0 1.0 N1 B:E44505 2.6 37.0 1.0 CD2 B:LEU240 3.2 21.0 1.0 CB B:ALA248 3.6 38.5 1.0 CG B:LEU240 3.7 27.5 1.0 O B:HOH641 3.8 45.2 1.0 C7 B:E44505 3.9 36.2 1.0 C2 B:E44505 3.9 38.0 1.0 CB B:CYS239 4.1 38.2 1.0 CB B:LEU253 4.1 27.2 1.0 CD2 B:LEU253 4.3 24.8 1.0 O B:ASP249 4.3 33.0 1.0 C6 B:E44505 4.4 39.0 1.0 N B:LEU240 4.5 40.4 1.0 CD1 B:LEU253 4.5 23.5 1.0 CG B:LEU253 4.5 26.5 1.0 C B:CYS239 4.5 44.3 1.0 CD1 B:LEU240 4.5 28.7 1.0 O B:VAL236 4.6 34.9 1.0 N B:ASP249 4.6 40.6 1.0 C B:ALA248 4.7 39.6 1.0 C B:ASP249 4.7 34.9 1.0 CA B:ALA248 4.8 44.3 1.0 O B:CYS239 4.8 50.1 1.0 O B:HOH619 4.8 35.3 1.0 CA B:CYS239 4.8 37.1 1.0 CB B:LEU240 4.9 25.2 1.0 N3 B:E44505 5.0 33.2 1.0 CA B:ASP249 5.0 40.0 1.0

Chlorine binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl502 b:58.6 occ:1.00 CL1 D:E44502 0.0 58.6 1.0 C1 D:E44502 1.7 54.1 1.0 N1 D:E44502 2.6 50.7 1.0 N4 D:E44502 2.6 50.8 1.0 CD2 D:LEU240 3.5 35.5 1.0 CB D:ALA248 3.9 49.4 1.0 C7 D:E44502 3.9 46.6 1.0 CB D:LEU253 3.9 39.4 1.0 C2 D:E44502 3.9 49.0 1.0 CG D:LEU240 4.0 38.4 1.0 CD2 D:LEU253 4.1 40.8 1.0 O D:HOH623 4.1 59.6 1.0 CD1 D:LEU253 4.2 39.1 1.0 O D:ASP249 4.2 41.6 1.0 CG D:LEU253 4.2 40.0 1.0 CB D:CYS239 4.4 60.8 1.0 C6 D:E44502 4.4 48.4 1.0 O D:VAL236 4.5 51.3 1.0 C D:ASP249 4.7 40.4 1.0 N D:ASP249 4.7 46.4 1.0 N D:LEU240 4.7 47.1 1.0 C D:CYS239 4.8 50.9 1.0 C D:ALA248 4.8 51.0 1.0 CD1 D:LEU240 4.9 37.7 1.0 CA D:LEU253 5.0 37.2 1.0 N3 D:E44502 5.0 38.3 1.0

S.Banerjee, K.E.Arnst, Y.Wang, G.Kumar, S.Deng, L.Yang, G.B.Li, J.Yang, S.W.White, W.Li, D.D.Miller. Heterocyclic-Fused Pyrimidines As Novel Tubulin Polymerization Inhibitors Targeting the Colchicine Binding Site: Structural Basis and Antitumor Efficacy. J. Med. Chem. V. 61 1704 2018.
ISSN: ISSN 1520-4804
PubMed: 29406710
DOI: 10.1021/ACS.JMEDCHEM.7B01858