Chlorine in PDB 6x1e: Tubulin-RB3_SLD-Ttl in Complex with Compound 5L

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5L, PDB code: 6x1e was solved by S.W.White, M.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.91 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.36, 157.742, 182.163, 90, 90, 90
R / Rfree (%)	17 / 22.4

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5L also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Calcium	(Ca)	2 atoms

The binding sites of Chlorine atom in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5L (pdb code 6x1e). 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 Compound 5L, PDB code: 6x1e:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5L


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 Compound 5L within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl505 b:70.9 occ:1.00 CL01 B:Y5L505 0.0 70.9 1.0 C02 B:Y5L505 1.8 41.6 1.0 N23 B:Y5L505 2.7 36.0 1.0 N03 B:Y5L505 2.7 35.5 1.0 CD2 B:LEU240 3.5 27.4 1.0 CG B:LEU240 3.7 27.1 1.0 CB B:CYS239 3.9 56.9 1.0 CB B:ALA248 3.9 40.8 1.0 C09 B:Y5L505 3.9 33.5 1.0 C04 B:Y5L505 4.0 45.4 1.0 O B:VAL236 4.0 64.1 1.0 CD2 B:LEU253 4.3 30.4 1.0 CD1 B:LEU253 4.3 31.1 1.0 N B:LEU240 4.4 51.7 1.0 C B:CYS239 4.5 49.9 1.0 CD1 B:LEU240 4.5 26.3 1.0 C05 B:Y5L505 4.5 41.4 1.0 CA B:CYS239 4.6 41.4 1.0 CG B:LEU253 4.6 33.7 1.0 CB B:LEU253 4.6 35.5 1.0 N B:CYS239 4.8 45.2 1.0 O B:ASP249 4.9 27.6 1.0 CB B:LEU240 4.9 43.1 1.0 O B:CYS239 4.9 67.1 1.0

Chlorine binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5L


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 Compound 5L within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl503 b:101.5 occ:1.00 CL01 D:Y5L503 0.0 101.5 1.0 C02 D:Y5L503 1.8 65.6 1.0 N03 D:Y5L503 2.7 50.7 1.0 N23 D:Y5L503 2.7 62.0 1.0 CD2 D:LEU240 3.5 35.6 1.0 CB D:ALA248 3.6 51.8 1.0 CG D:LEU240 3.8 37.0 1.0 O D:VAL236 3.9 60.0 1.0 CB D:CYS239 3.9 53.7 1.0 C04 D:Y5L503 3.9 50.5 1.0 C09 D:Y5L503 4.0 62.1 1.0 CD1 D:LEU253 4.2 32.4 1.0 N D:LEU240 4.4 47.4 1.0 CB D:LEU253 4.5 35.5 1.0 CD2 D:LEU253 4.5 33.5 1.0 C05 D:Y5L503 4.5 66.1 1.0 C D:CYS239 4.6 51.8 1.0 CG D:LEU253 4.6 32.4 1.0 CA D:CYS239 4.7 52.9 1.0 CD1 D:LEU240 4.7 37.5 1.0 N D:CYS239 4.8 54.8 1.0 CA D:ALA248 4.9 33.4 1.0 SG D:CYS239 4.9 72.3 1.0 CB D:LEU240 5.0 38.2 1.0

S.Banerjee, F.Mahmud, S.Deng, L.Ma, M.K.Yun, S.O.Fakayode, K.E.Arnst, L.Yang, H.Chen, Z.Wu, P.B.Lukka, K.Parmar, B.Meibohm, S.W.White, Y.Wang, W.Li, D.D.Miller. X-Ray Crystallography-Guided Design, Antitumor Efficacy, and Qsar Analysis of Metabolically Stable Cyclopenta-Pyrimidinyl Dihydroquinoxalinone As A Potent Tubulin Polymerization Inhibitor. J.Med.Chem. V. 64 13072 2021.
ISSN: ISSN 0022-2623
PubMed: 34406768
DOI: 10.1021/ACS.JMEDCHEM.1C01202