Chlorine in PDB 6br1: Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4A

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4A, PDB code: 6br1 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)	49.64 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.927, 157.613, 180.989, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.5

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 4A 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 4A (pdb code 6br1). 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 4A, PDB code: 6br1:
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 4A


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl505 b:50.7 occ:1.00 CL1 B:E3Y505 0.0 50.7 1.0 C1 B:E3Y505 1.7 37.4 1.0 N1 B:E3Y505 2.6 32.2 1.0 N4 B:E3Y505 2.6 34.8 1.0 CD2 B:LEU240 3.3 25.2 1.0 CB B:ALA248 3.6 47.0 1.0 CG B:LEU240 3.8 29.0 1.0 C7 B:E3Y505 3.9 27.7 1.0 C2 B:E3Y505 3.9 28.9 1.0 O B:HOH675 4.0 38.4 1.0 CB B:CYS239 4.1 40.1 1.0 O B:ASP249 4.1 25.4 1.0 CB B:LEU253 4.2 25.8 1.0 CD1 B:LEU253 4.3 22.0 1.0 CD2 B:LEU253 4.3 25.3 1.0 C6 B:E3Y505 4.4 26.5 1.0 CG B:LEU253 4.5 28.5 1.0 N B:LEU240 4.5 42.0 1.0 CD1 B:LEU240 4.6 25.8 1.0 C B:ASP249 4.6 28.1 1.0 N B:ASP249 4.6 34.7 1.0 C B:CYS239 4.6 45.3 1.0 O B:VAL236 4.7 41.2 1.0 C B:ALA248 4.7 40.4 1.0 CA B:ALA248 4.8 51.0 1.0 CA B:CYS239 4.9 39.6 1.0 CA B:ASP249 4.9 30.9 1.0 N2 B:E3Y505 4.9 31.8 1.0 CB B:LEU240 5.0 35.5 1.0 N3 B:E3Y505 5.0 28.1 1.0 O B:CYS239 5.0 50.9 1.0

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


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 4A within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl502 b:60.8 occ:1.00 CL1 D:E3Y502 0.0 60.8 1.0 C1 D:E3Y502 1.7 55.8 1.0 N4 D:E3Y502 2.6 51.8 1.0 N1 D:E3Y502 2.6 50.7 1.0 CD2 D:LEU240 3.5 28.9 1.0 CG D:LEU240 3.8 30.5 1.0 CB D:ALA248 3.8 33.5 1.0 C7 D:E3Y502 3.9 43.1 1.0 C2 D:E3Y502 3.9 46.8 1.0 CB D:LEU253 3.9 32.5 1.0 CD1 D:LEU253 4.1 31.0 1.0 CD2 D:LEU253 4.1 34.3 1.0 O D:HOH630 4.2 54.3 1.0 CG D:LEU253 4.2 33.5 1.0 O D:ASP249 4.2 35.8 1.0 CB D:CYS239 4.3 48.7 1.0 O D:VAL236 4.4 43.8 1.0 C6 D:E3Y502 4.4 45.3 1.0 CD1 D:LEU240 4.6 30.1 1.0 N D:LEU240 4.6 40.8 1.0 C D:ASP249 4.7 35.5 1.0 N D:ASP249 4.8 38.6 1.0 O D:HOH605 4.8 41.7 1.0 C D:CYS239 4.8 39.6 1.0 C D:ALA248 4.9 40.0 1.0 N2 D:E3Y502 5.0 43.7 1.0 N3 D:E3Y502 5.0 34.6 1.0 CA D:ALA248 5.0 41.0 1.0 CA D:LEU253 5.0 30.5 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