Zinc in PDB 7pjk: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with A Benzotriazole Analog of Thalidomide

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with A Benzotriazole Analog of Thalidomide, PDB code: 7pjk was solved by C.Heim, M.D.Hartmann, S.Maiwald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.44 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.779, 59.435, 88.189, 90, 90, 90
R / Rfree (%)	20.9 / 25.4

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with A Benzotriazole Analog of Thalidomide (pdb code 7pjk). 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 A Benzotriazole Analog of Thalidomide, PDB code: 7pjk:
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 A Benzotriazole Analog of Thalidomide


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 A Benzotriazole Analog of Thalidomide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:40.2 occ:1.00 SG A:CYS93 2.3 41.1 1.0 SG A:CYS24 2.3 38.3 1.0 SG A:CYS27 2.3 40.7 1.0 SG A:CYS90 2.3 40.7 1.0 CB A:CYS90 3.1 39.9 1.0 CB A:CYS24 3.1 37.6 1.0 CB A:CYS93 3.3 42.0 1.0 CB A:CYS27 3.4 42.6 1.0 N A:CYS93 3.9 41.1 1.0 N A:CYS27 3.9 42.8 1.0 CA A:CYS93 4.1 42.3 1.0 CA A:CYS27 4.2 42.7 1.0 CB A:GLN26 4.4 48.0 1.0 CB A:GLN29 4.6 40.6 1.0 CA A:CYS24 4.6 37.0 1.0 CA A:CYS90 4.6 39.1 1.0 CB A:SER95 4.6 44.0 1.0 CB A:GLN92 4.7 40.4 1.0 C A:GLN26 4.7 44.6 1.0 C A:CYS93 4.8 42.1 1.0 C A:CYS27 4.9 42.2 1.0 N A:GLY28 4.9 41.4 1.0 C A:GLN92 4.9 41.6 1.0 N A:GLY94 4.9 41.8 1.0 CA A:GLN26 4.9 46.1 1.0 N A:GLN26 5.0 41.9 1.0 C A:CYS24 5.0 38.0 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with A Benzotriazole Analog of Thalidomide


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 A Benzotriazole Analog of Thalidomide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:60.4 occ:1.00 SG B:CYS90 2.3 58.3 1.0 SG B:CYS27 2.3 63.2 1.0 SG B:CYS93 2.3 60.4 1.0 SG B:CYS24 2.3 56.2 1.0 CB B:CYS24 3.1 54.6 1.0 CB B:CYS90 3.2 53.7 1.0 CB B:CYS93 3.3 63.8 1.0 CB B:CYS27 3.4 66.3 1.0 N B:CYS93 3.8 61.4 1.0 N B:CYS27 3.9 65.1 1.0 CA B:CYS93 4.1 63.3 1.0 CA B:CYS27 4.2 66.3 1.0 CB B:GLN92 4.5 62.5 1.0 CA B:CYS24 4.5 53.1 1.0 CA B:CYS90 4.6 50.8 1.0 CB B:GLN26 4.6 67.5 1.0 C B:GLN26 4.8 67.1 1.0 CB B:GLN29 4.8 59.3 1.0 C B:GLN92 4.8 63.1 1.0 C B:CYS27 4.8 64.6 1.0 C B:CYS93 4.8 61.7 1.0 CB B:SER95 4.8 57.2 1.0 N B:GLY28 4.9 61.8 1.0 N B:GLY94 5.0 59.4 1.0 C B:CYS24 5.0 55.8 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with A Benzotriazole Analog of Thalidomide


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 A Benzotriazole Analog of Thalidomide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:60.2 occ:1.00 SG C:CYS90 2.3 60.5 1.0 SG C:CYS93 2.3 61.3 1.0 SG C:CYS27 2.3 58.9 1.0 SG C:CYS24 2.3 65.2 1.0 CB C:CYS90 3.2 63.4 1.0 CB C:CYS24 3.2 65.3 1.0 CB C:CYS27 3.3 60.0 1.0 CB C:CYS93 3.4 60.1 1.0 N C:CYS27 3.7 64.6 1.0 N C:CYS93 3.8 58.5 1.0 CA C:CYS27 4.1 61.6 1.0 CA C:CYS93 4.1 60.1 1.0 CB C:GLN92 4.4 54.2 1.0 CB C:GLN29 4.4 57.1 1.0 CB C:GLN26 4.5 72.5 1.0 N C:GLY28 4.5 60.2 1.0 CA C:CYS24 4.6 68.2 1.0 CB C:SER95 4.6 72.6 1.0 CA C:CYS90 4.6 63.6 1.0 C C:CYS27 4.7 60.5 1.0 C C:GLN26 4.7 67.7 1.0 C C:GLN92 4.8 56.9 1.0 N C:GLN29 4.8 57.6 1.0 C C:CYS93 4.8 63.0 1.0 N C:GLY94 4.9 63.8 1.0 CA C:GLN26 5.0 71.2 1.0 N C:GLN26 5.0 71.8 1.0 CA C:GLN92 5.0 55.6 1.0 C C:CYS24 5.0 69.8 1.0

M.Krasavin, A.Bubyrev, A.Kazantsev, C.Heim, S.Maiwald, D.Zhukovsky, D.Dar'in, M.D.Hartmann, A.Bunev. Replacing the Phthalimide Core in Thalidomide with Benzotriazole. J Enzyme Inhib Med Chem V. 37 527 2022.
ISSN: ESSN 1475-6374
PubMed: 35220840
DOI: 10.1080/14756366.2021.2024525