Zinc in PDB 8rdq: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B, PDB code: 8rdq was solved by L.Bischof, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.61 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.536, 59.8, 88.01, 90, 90, 90
R / Rfree (%)	20.5 / 24.9

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B (pdb code 8rdq). 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 Spiro-Isoxazol Based Compound 8B, PDB code: 8rdq:
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 Spiro-Isoxazol Based Compound 8B


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 Spiro-Isoxazol Based Compound 8B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:31.5 occ:1.00 SG A:CYS24 2.3 31.1 1.0 SG A:CYS93 2.3 32.0 1.0 SG A:CYS27 2.3 31.9 1.0 SG A:CYS90 2.3 31.3 1.0 CB A:CYS24 3.1 29.9 1.0 CB A:CYS90 3.1 30.0 1.0 CB A:CYS93 3.3 32.2 1.0 CB A:CYS27 3.4 34.5 1.0 N A:CYS93 3.8 32.4 1.0 N A:CYS27 3.9 34.8 1.0 CA A:CYS93 4.1 33.1 1.0 CA A:CYS27 4.2 34.6 1.0 CB A:GLN29 4.4 31.2 1.0 CB A:GLN26 4.4 41.3 1.0 CA A:CYS24 4.5 29.1 1.0 CA A:CYS90 4.6 29.3 1.0 CB A:GLN92 4.7 30.5 1.0 CB A:SER95 4.7 35.7 1.0 C A:GLN26 4.7 36.4 1.0 C A:CYS93 4.8 32.8 1.0 C A:CYS27 4.9 34.5 1.0 N A:GLY28 4.9 33.7 1.0 N A:GLY94 4.9 33.0 1.0 C A:GLN92 4.9 32.0 1.0 N A:GLN29 4.9 32.4 1.0 N A:GLN26 4.9 36.0 1.0 CA A:GLN26 4.9 38.8 1.0 C A:CYS24 5.0 30.4 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B


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 Spiro-Isoxazol Based Compound 8B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:37.3 occ:1.00 SG B:CYS90 2.3 37.5 1.0 SG B:CYS93 2.3 37.1 1.0 SG B:CYS24 2.3 35.4 1.0 SG B:CYS27 2.3 38.7 1.0 CB B:CYS24 3.1 34.5 1.0 CB B:CYS90 3.1 35.2 1.0 CB B:CYS93 3.3 39.6 1.0 CB B:CYS27 3.4 41.2 1.0 N B:CYS93 3.7 38.1 1.0 N B:CYS27 3.9 40.2 1.0 CA B:CYS93 4.0 39.6 1.0 CA B:CYS27 4.2 41.1 1.0 CA B:CYS24 4.5 34.3 1.0 CB B:GLN92 4.5 38.1 1.0 CA B:CYS90 4.6 33.7 1.0 CB B:GLN26 4.6 39.2 1.0 CB B:GLN29 4.7 42.3 1.0 CB B:SER95 4.7 38.1 1.0 C B:GLN92 4.7 38.8 1.0 C B:CYS93 4.7 39.0 1.0 C B:GLN26 4.8 40.6 1.0 C B:CYS27 4.8 40.3 1.0 N B:GLY94 4.9 38.1 1.0 N B:GLY28 4.9 38.9 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B


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 Spiro-Isoxazol Based Compound 8B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:42.5 occ:1.00 SG C:CYS93 2.3 44.2 1.0 SG C:CYS90 2.3 41.3 1.0 SG C:CYS27 2.3 45.0 1.0 SG C:CYS24 2.4 43.7 1.0 CB C:CYS90 3.1 42.4 1.0 CB C:CYS24 3.2 43.9 1.0 CB C:CYS93 3.3 44.1 1.0 CB C:CYS27 3.4 47.4 1.0 N C:CYS93 3.7 42.9 1.0 N C:CYS27 3.8 50.3 1.0 CA C:CYS93 4.0 44.1 1.0 CA C:CYS27 4.1 48.9 1.0 CB C:GLN29 4.4 41.5 1.0 CB C:GLN26 4.5 54.8 1.0 CA C:CYS90 4.5 42.5 1.0 CB C:SER95 4.6 49.2 1.0 CA C:CYS24 4.6 44.9 1.0 CB C:GLN92 4.6 41.5 1.0 C C:CYS93 4.7 44.6 1.0 C C:GLN26 4.7 53.0 1.0 C C:GLN92 4.8 42.9 1.0 N C:GLY94 4.8 44.5 1.0 C C:CYS27 4.8 47.2 1.0 N C:GLY28 4.8 45.9 1.0 N C:GLN29 4.9 42.2 1.0 N C:SER95 4.9 47.8 1.0

R.Shevalev, L.Bischof, A.Sapegin, A.Bunev, G.Olga, G.Kantin, S.Kalinin, M.D.Hartmann. Discovery and Characterization of Potent Spiro-Isoxazole-Based Cereblon Ligands with A Novel Binding Mode. Eur.J.Med.Chem. V. 270 16328 2024.
ISSN: ISSN 0223-5234
PubMed: 38552426
DOI: 10.1016/J.EJMECH.2024.116328