Zinc in PDB 6r1x: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7A

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7A, PDB code: 6r1x 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)	49.03 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.333, 58.675, 89.272, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.6

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7A (pdb code 6r1x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7A, PDB code: 6r1x:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:22.4 occ:1.00 SG A:CYS93 2.3 23.5 1.0 SG A:CYS27 2.3 22.2 1.0 SG A:CYS24 2.3 23.0 1.0 SG A:CYS90 2.3 21.3 1.0 CB A:CYS90 3.1 21.2 1.0 CB A:CYS24 3.2 21.6 1.0 CB A:CYS93 3.3 24.3 1.0 CB A:CYS27 3.5 24.3 1.0 N A:CYS93 3.8 23.6 1.0 N A:CYS27 3.8 25.0 1.0 CA A:CYS93 4.0 24.1 1.0 CA A:CYS27 4.2 25.2 1.0 CB A:GLN26 4.4 31.3 1.0 CB A:GLN29 4.5 23.2 1.0 CA A:CYS24 4.6 21.7 1.0 CB A:SER95 4.6 26.9 1.0 CA A:CYS90 4.6 20.8 1.0 C A:GLN26 4.6 28.8 1.0 CB A:GLN92 4.7 23.9 1.0 C A:CYS93 4.8 24.4 1.0 C A:GLN92 4.8 24.2 1.0 N A:GLN26 4.9 27.1 1.0 CA A:GLN26 4.9 28.2 1.0 N A:GLY94 4.9 23.4 1.0 C A:CYS27 4.9 24.9 1.0 N A:GLY28 4.9 23.6 1.0 N A:GLN29 5.0 22.6 1.0 C A:CYS24 5.0 22.1 1.0 N A:SER95 5.0 23.7 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:28.4 occ:1.00 SG B:CYS93 2.3 28.6 1.0 SG B:CYS90 2.3 27.2 1.0 SG B:CYS27 2.3 29.6 1.0 SG B:CYS24 2.4 26.4 1.0 CB B:CYS90 3.1 25.2 1.0 CB B:CYS24 3.2 26.3 1.0 CB B:CYS27 3.3 30.1 1.0 CB B:CYS93 3.3 29.8 1.0 N B:CYS93 3.7 28.7 1.0 N B:CYS27 3.9 32.7 1.0 CA B:CYS93 4.1 29.0 1.0 CA B:CYS27 4.1 31.0 1.0 CA B:CYS90 4.6 24.2 1.0 CA B:CYS24 4.6 25.8 1.0 CB B:GLN92 4.6 30.2 1.0 CB B:GLN26 4.7 36.5 1.0 C B:GLN92 4.8 30.2 1.0 CB B:SER95 4.8 27.3 1.0 CB B:GLN29 4.8 31.1 1.0 C B:GLN26 4.8 34.1 1.0 C B:CYS93 4.8 29.8 1.0 C B:CYS27 4.8 31.1 1.0 N B:GLY28 4.9 28.8 1.0 N B:GLY94 4.9 28.1 1.0 N B:GLN29 5.0 28.1 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:31.3 occ:1.00 SG C:CYS27 2.3 30.1 1.0 SG C:CYS24 2.3 35.5 1.0 SG C:CYS93 2.3 33.1 1.0 SG C:CYS90 2.3 30.2 1.0 CB C:CYS24 3.2 34.9 1.0 CB C:CYS90 3.2 31.5 1.0 CB C:CYS93 3.3 32.9 1.0 CB C:CYS27 3.4 32.8 1.0 N C:CYS93 3.7 31.5 1.0 N C:CYS27 3.8 36.8 1.0 CA C:CYS93 4.1 32.9 1.0 CA C:CYS27 4.1 34.4 1.0 CB C:GLN29 4.4 29.9 1.0 CB C:GLN92 4.6 27.6 1.0 CA C:CYS24 4.6 35.1 1.0 CB C:SER95 4.6 41.4 1.0 CB C:GLN26 4.7 44.4 1.0 CA C:CYS90 4.7 31.5 1.0 C C:CYS27 4.7 33.8 1.0 C C:CYS93 4.7 34.2 1.0 C C:GLN26 4.7 40.4 1.0 C C:GLN92 4.8 29.9 1.0 N C:GLY28 4.8 32.5 1.0 N C:GLN29 4.8 30.3 1.0 N C:GLY94 4.8 33.7 1.0 N C:SER95 4.9 38.5 1.0 N C:GLN26 5.0 42.3 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