Chlorine in PDB 6r0u: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product, PDB code: 6r0u was solved by C.Heim, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.98 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.952, 59.583, 89.053, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.7

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Chlorine atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product (pdb code 6r0u). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product, PDB code: 6r0u:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:57.6 occ:1.00 OD2 A:ASP116 3.0 39.3 1.0 OD1 A:ASP116 3.2 40.4 1.0 NH2 A:ARG117 3.4 31.5 1.0 NE A:ARG117 3.4 27.4 1.0 CG A:ASP116 3.5 33.7 1.0 CZ A:ARG117 3.9 30.1 1.0 O A:HOH306 3.9 42.0 1.0 O A:HOH352 4.1 26.8 1.0 CG2 A:ILE114 4.3 21.2 1.0 CG A:ARG117 4.5 25.4 1.0 CD A:ARG117 4.6 25.4 1.0

Chlorine binding site 2 out of 2 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl204 b:57.3 occ:1.00 OD2 B:ASP116 2.8 28.7 0.6 OD1 B:ASP116 3.4 28.9 0.6 NE B:ARG57 3.4 30.4 1.0 CG B:ASP116 3.4 29.2 0.6 NH2 B:ARG57 3.7 32.1 1.0 NH2 A:ARG25 3.7 27.1 1.0 OD2 B:ASP116 3.9 30.0 0.4 O B:HOH324 4.0 26.9 1.0 CZ B:ARG57 4.0 31.5 1.0 CB B:ARG57 4.2 25.2 1.0 O B:HOH350 4.3 28.1 1.0 CD B:ARG57 4.4 28.0 1.0 O A:HOH336 4.4 39.9 1.0 CG B:ASP116 4.6 29.2 0.4 CB B:ASP116 4.6 29.2 0.4 CB B:ASP116 4.9 28.9 0.6 CG B:ARG57 4.9 25.8 1.0 CZ A:ARG25 5.0 24.4 1.0

C.Heim, D.Pliatsika, F.Mousavizadeh, K.Bar, B.Hernandez Alvarez, A.Giannis, M.D.Hartmann. De-Novo Design of Cereblon (Crbn) Effectors Guided By Natural Hydrolysis Products of Thalidomide Derivatives. J.Med.Chem. V. 62 6615 2019.
ISSN: ISSN 0022-2623
PubMed: 31251063
DOI: 10.1021/ACS.JMEDCHEM.9B00454