Chlorine in PDB 6bry: Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A, PDB code: 6bry 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)	49.75 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.089, 157.766, 181.456, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.6

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A 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 6A (pdb code 6bry). 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 6A, PDB code: 6bry:
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 6A


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 6A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl504 b:49.2 occ:1.00 CL1 B:GK9504 0.0 49.2 1.0 C1 B:GK9504 1.7 42.0 1.0 N3 B:GK9504 2.6 36.8 1.0 N1 B:GK9504 2.6 34.6 1.0 O B:HOH622 3.4 37.7 1.0 CD2 B:LEU240 3.5 18.7 1.0 CG B:LEU240 3.8 26.0 1.0 CB B:ALA248 3.8 33.5 1.0 C6 B:GK9504 3.8 32.5 1.0 CB B:CYS239 3.8 34.6 1.0 C2 B:GK9504 3.8 28.6 1.0 O B:VAL236 4.1 39.0 1.0 CD2 B:LEU253 4.3 15.3 1.0 N B:LEU240 4.3 38.3 1.0 C B:CYS239 4.4 39.5 1.0 C3 B:GK9504 4.4 27.0 1.0 CD1 B:LEU253 4.4 15.3 1.0 CB B:LEU253 4.5 16.2 1.0 CA B:CYS239 4.5 33.6 1.0 CD1 B:LEU240 4.6 25.4 1.0 CG B:LEU253 4.6 17.1 1.0 O B:CYS239 4.7 46.2 1.0 O B:HOH607 4.7 28.4 1.0 O B:ASP249 4.8 33.0 1.0 N B:CYS239 4.8 28.4 1.0 CB B:LEU240 4.9 31.4 1.0 N2 B:GK9504 5.0 33.1 1.0

Chlorine binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 6A


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 6A within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl502 b:72.5 occ:1.00 CL1 D:GK9502 0.0 72.5 1.0 C1 D:GK9502 1.7 54.3 1.0 N3 D:GK9502 2.6 46.9 1.0 N1 D:GK9502 2.6 44.4 1.0 CD2 D:LEU240 3.5 39.1 1.0 C2 D:GK9502 3.8 43.6 1.0 C6 D:GK9502 3.9 40.5 1.0 CG D:LEU240 3.9 42.2 1.0 CB D:CYS239 3.9 48.2 1.0 CB D:ALA248 3.9 39.2 1.0 O D:VAL236 3.9 50.5 1.0 CB D:LEU253 4.3 36.4 1.0 CD1 D:LEU253 4.3 26.9 1.0 C3 D:GK9502 4.4 43.0 1.0 N D:LEU240 4.4 48.5 1.0 CD2 D:LEU253 4.5 29.3 1.0 CG D:LEU253 4.5 31.6 1.0 C D:CYS239 4.5 44.4 1.0 CD1 D:LEU240 4.6 40.9 1.0 CA D:CYS239 4.6 44.1 1.0 O D:ASP249 4.8 38.3 1.0 N D:CYS239 4.9 46.5 1.0 N2 D:GK9502 5.0 33.1 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