Zinc in PDB 8aoq: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 20A

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 20A, PDB code: 8aoq 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)	49.16 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.66, 59.169, 88.334, 90, 90, 90
R / Rfree (%)	19.5 / 23.3

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 20A (pdb code 8aoq). 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 20A, PDB code: 8aoq:
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 20A


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 20A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:39.0 occ:1.00 SG A:CYS93 2.3 38.9 1.0 SG A:CYS24 2.3 37.2 1.0 SG A:CYS90 2.3 39.1 1.0 SG A:CYS27 2.3 39.5 1.0 CB A:CYS90 3.0 39.8 1.0 CB A:CYS24 3.1 36.1 1.0 CB A:CYS93 3.3 40.0 1.0 CB A:CYS27 3.4 41.7 1.0 N A:CYS93 3.8 39.4 1.0 N A:CYS27 3.9 40.3 1.0 CA A:CYS93 4.1 41.1 1.0 CA A:CYS27 4.2 40.6 1.0 CB A:GLN26 4.4 49.6 1.0 CB A:GLN29 4.5 43.1 1.0 CA A:CYS90 4.5 38.5 1.0 CA A:CYS24 4.5 35.2 1.0 CB A:SER95 4.6 43.5 1.0 C A:GLN26 4.7 42.0 1.0 CB A:GLN92 4.7 39.3 1.0 C A:CYS93 4.8 39.6 1.0 CA A:GLN26 4.9 44.8 1.0 C A:GLN92 4.9 40.5 1.0 C A:CYS27 4.9 40.5 1.0 N A:GLN26 4.9 39.0 1.0 N A:GLY28 4.9 38.6 1.0 N A:GLY94 4.9 39.8 1.0 C A:CYS24 5.0 36.7 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 20A


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 20A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:82.2 occ:1.00 SG B:CYS90 2.3 74.6 1.0 SG B:CYS27 2.4 83.9 1.0 SG B:CYS24 2.4 70.5 1.0 SG B:CYS93 2.4 78.7 1.0 CB B:CYS90 3.0 63.9 1.0 CB B:CYS24 3.1 64.4 1.0 CB B:CYS27 3.4 85.0 1.0 CB B:CYS93 3.4 79.9 1.0 N B:CYS27 3.8 79.9 1.0 N B:CYS93 3.9 74.2 1.0 CA B:CYS27 4.1 82.9 1.0 CA B:CYS93 4.2 77.3 1.0 CB B:GLN26 4.4 80.1 1.0 CA B:CYS90 4.5 57.0 1.0 CB B:GLN92 4.5 75.9 1.0 CA B:CYS24 4.6 59.1 1.0 C B:GLN26 4.6 81.3 1.0 CB B:GLN29 4.8 69.3 1.0 C B:CYS27 4.8 80.0 1.0 C B:GLN92 4.9 76.5 1.0 C B:CYS93 4.9 74.1 1.0 N B:GLY28 4.9 75.3 1.0 CA B:GLN26 4.9 78.2 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 20A


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 20A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:66.5 occ:1.00 SG C:CYS93 2.3 69.0 1.0 SG C:CYS90 2.3 65.8 1.0 SG C:CYS27 2.4 64.6 1.0 SG C:CYS24 2.4 72.4 1.0 CB C:CYS24 3.1 73.0 1.0 CB C:CYS90 3.3 70.9 1.0 CB C:CYS27 3.3 67.6 1.0 CB C:CYS93 3.4 67.2 1.0 N C:CYS93 3.7 66.5 1.0 N C:CYS27 3.7 73.2 1.0 CA C:CYS27 4.0 70.7 1.0 CA C:CYS93 4.1 67.5 1.0 CB C:GLN29 4.4 66.5 1.0 CB C:GLN92 4.4 63.3 1.0 CB C:GLN26 4.4 81.3 1.0 N C:GLY28 4.6 70.4 1.0 CA C:CYS24 4.6 76.3 1.0 C C:GLN26 4.7 77.8 1.0 C C:CYS27 4.7 70.5 1.0 C C:CYS93 4.7 70.3 1.0 CA C:CYS90 4.7 72.4 1.0 C C:GLN92 4.7 64.6 1.0 N C:GLY94 4.7 71.9 1.0 CB C:SER95 4.7 80.0 1.0 N C:GLN29 4.8 67.0 1.0 CA C:GLN92 4.9 64.0 1.0 CA C:GLN26 4.9 79.8 1.0 N C:SER95 4.9 78.0 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