Zinc in PDB 8aop: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R, PDB code: 8aop was solved by S.Maiwald, C.Heim, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.70 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.79, 59.194, 87.861, 90, 90, 90
R / Rfree (%)	19.7 / 22.7

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R (pdb code 8aop). 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 14R, PDB code: 8aop:
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 14R


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 14R within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:38.9 occ:1.00 SG A:CYS24 2.3 36.2 1.0 SG A:CYS93 2.3 39.9 1.0 SG A:CYS90 2.3 38.4 1.0 SG A:CYS27 2.3 42.0 1.0 CB A:CYS90 3.1 39.3 1.0 CB A:CYS24 3.1 36.5 1.0 CB A:CYS93 3.3 41.5 1.0 CB A:CYS27 3.4 43.0 1.0 N A:CYS93 3.8 40.5 1.0 N A:CYS27 3.9 39.9 1.0 CA A:CYS93 4.1 41.4 1.0 CA A:CYS27 4.2 42.0 1.0 CB A:SER95 4.5 40.5 1.0 CB A:GLN29 4.5 39.4 0.5 CB A:GLN26 4.5 47.1 1.0 CA A:CYS90 4.5 38.9 1.0 CA A:CYS24 4.5 35.7 1.0 CB A:GLN29 4.6 41.8 0.5 C A:GLN26 4.6 42.6 1.0 CB A:GLN92 4.7 40.5 1.0 C A:CYS93 4.8 41.2 1.0 C A:CYS27 4.9 41.9 1.0 N A:GLN26 4.9 39.8 1.0 CA A:GLN26 4.9 44.6 1.0 C A:GLN92 4.9 41.3 1.0 N A:SER95 4.9 39.4 1.0 N A:GLY94 4.9 40.9 1.0 C A:CYS24 5.0 36.8 1.0 N A:GLY28 5.0 39.3 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R


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 14R within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:68.5 occ:1.00 SG B:CYS90 2.3 65.5 1.0 SG B:CYS24 2.4 62.9 1.0 SG B:CYS27 2.4 72.9 1.0 SG B:CYS93 2.4 72.1 1.0 CB B:CYS90 3.0 57.5 1.0 CB B:CYS24 3.1 59.5 1.0 CB B:CYS27 3.3 75.4 1.0 CB B:CYS93 3.5 73.7 1.0 N B:CYS27 3.9 72.6 1.0 N B:CYS93 3.9 70.1 1.0 CA B:CYS27 4.1 74.9 1.0 CA B:CYS93 4.2 72.3 1.0 CA B:CYS90 4.4 53.3 1.0 CB B:GLN92 4.5 71.0 1.0 CA B:CYS24 4.6 55.6 1.0 C B:GLN26 4.7 75.5 1.0 CB B:GLN26 4.8 77.2 1.0 C B:CYS27 4.8 71.7 1.0 C B:GLN92 4.9 72.1 1.0 CB B:GLN29 4.9 66.7 1.0 CB B:SER95 4.9 57.9 1.0 C B:CYS93 4.9 69.0 1.0 N B:GLY28 4.9 66.8 1.0 C B:CYS90 5.0 54.6 1.0 N B:GLY94 5.0 66.2 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R


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 14R within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:58.1 occ:1.00 SG C:CYS24 2.3 63.1 1.0 SG C:CYS90 2.3 58.9 1.0 SG C:CYS27 2.3 58.3 1.0 SG C:CYS93 2.4 60.6 1.0 CB C:CYS24 3.1 62.8 1.0 CB C:CYS90 3.2 61.9 1.0 CB C:CYS27 3.3 60.3 1.0 CB C:CYS93 3.4 60.1 1.0 N C:CYS27 3.7 65.2 1.0 N C:CYS93 3.8 59.6 1.0 CA C:CYS27 4.1 62.1 1.0 CA C:CYS93 4.1 60.4 1.0 CB C:GLN29 4.4 59.1 1.0 CB C:GLN26 4.5 71.9 1.0 CB C:SER95 4.6 70.0 1.0 CB C:GLN92 4.6 55.5 1.0 N C:GLY28 4.6 61.4 1.0 CA C:CYS24 4.6 65.0 1.0 CA C:CYS90 4.6 63.0 1.0 C C:CYS27 4.7 62.0 1.0 C C:GLN26 4.7 67.7 1.0 C C:GLN92 4.8 57.1 1.0 C C:CYS93 4.8 62.6 1.0 N C:GLN29 4.8 59.8 1.0 N C:GLY94 4.8 64.1 1.0 N C:SER95 4.9 68.4 1.0 CA C:GLN26 5.0 70.0 1.0 N C:GLN26 5.0 69.2 1.0

M.Krasavin, M.Adamchik, A.Bubyrev, C.Heim, S.Maiwald, D.Zhukovsky, P.Zhmurov, A.Bunev, M.D.Hartmann. Synthesis of Novel Glutarimide Ligands For the E3 Ligase Substrate Receptor Cereblon (Crbn): Investigation of Their Binding Mode and Antiproliferative Effects Against Myeloma Cell Lines. Eur.J.Med.Chem. V. 246 14990 2023.
ISSN: ISSN 0223-5234
PubMed: 36476642
DOI: 10.1016/J.EJMECH.2022.114990