Zinc in PDB 8ou3: Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D, PDB code: 8ou3 was solved by C.Heim, L.Bischof, S.Maiwald, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.33 / 1.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.793, 59.519, 88.149, 90, 90, 90
R / Rfree (%)	21.5 / 23.8

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D (pdb code 8ou3). 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 in Complex with Novel Benzamide-Type Cereblon Binder 8D, PDB code: 8ou3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D


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 in Complex with Novel Benzamide-Type Cereblon Binder 8D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:21.5 occ:1.00 SG A:CYS24 2.3 20.9 1.0 SG A:CYS93 2.3 22.2 1.0 SG A:CYS27 2.3 22.2 1.0 SG A:CYS90 2.4 21.2 1.0 CB A:CYS24 3.1 19.7 1.0 CB A:CYS90 3.2 20.4 1.0 CB A:CYS93 3.3 20.5 1.0 CB A:CYS27 3.5 23.6 1.0 N A:CYS93 3.8 22.2 1.0 N A:CYS27 3.9 22.7 1.0 CA A:CYS93 4.1 22.4 1.0 CA A:CYS27 4.2 23.6 1.0 CB A:SER95 4.4 23.7 1.0 CA A:CYS24 4.5 19.0 1.0 CB A:GLN26 4.5 26.8 1.0 CB A:GLN29 4.6 21.4 1.0 CA A:CYS90 4.6 19.8 1.0 C A:GLN26 4.6 26.9 1.0 C A:CYS93 4.8 22.4 1.0 CB A:GLN92 4.8 23.7 1.0 N A:GLN26 4.8 21.9 1.0 N A:GLY94 4.9 21.7 1.0 C A:GLN92 4.9 22.3 1.0 C A:CYS27 4.9 24.1 1.0 CA A:GLN26 4.9 24.9 1.0 N A:SER95 4.9 21.5 1.0 N A:GLY28 4.9 21.6 1.0 C A:CYS24 4.9 21.0 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D


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 in Complex with Novel Benzamide-Type Cereblon Binder 8D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:26.5 occ:1.00 SG B:CYS93 2.3 28.6 1.0 SG B:CYS90 2.3 25.8 1.0 SG B:CYS24 2.4 26.0 1.0 SG B:CYS27 2.4 28.1 1.0 CB B:CYS90 3.1 24.8 1.0 CB B:CYS24 3.2 27.2 1.0 CB B:CYS93 3.3 30.0 1.0 CB B:CYS27 3.3 29.6 1.0 N B:CYS27 3.8 28.5 1.0 N B:CYS93 3.8 26.2 1.0 CA B:CYS93 4.1 27.9 1.0 CA B:CYS27 4.1 29.1 1.0 CA B:CYS90 4.6 22.9 1.0 CA B:CYS24 4.6 23.4 1.0 CB B:GLN92 4.7 26.5 1.0 CB B:SER95 4.7 27.7 1.0 C B:GLN26 4.7 30.7 1.0 C B:GLN92 4.7 25.4 1.0 C B:CYS27 4.7 28.7 1.0 C B:CYS93 4.8 29.1 1.0 CB B:GLN26 4.8 33.6 1.0 N B:GLY28 4.8 26.9 1.0 CB B:GLN29 4.9 30.8 1.0 N B:GLY94 4.9 29.6 1.0 N B:GLN29 5.0 27.9 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D


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 in Complex with Novel Benzamide-Type Cereblon Binder 8D within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:26.0 occ:1.00 SG C:CYS27 2.3 26.9 1.0 SG C:CYS93 2.3 27.1 1.0 SG C:CYS24 2.3 27.3 1.0 SG C:CYS90 2.4 25.6 1.0 CB C:CYS24 3.1 27.2 1.0 CB C:CYS90 3.2 25.6 1.0 CB C:CYS93 3.3 25.6 1.0 CB C:CYS27 3.4 31.5 1.0 N C:CYS93 3.8 25.2 1.0 N C:CYS27 3.8 31.5 1.0 CA C:CYS93 4.1 26.4 1.0 CA C:CYS27 4.1 32.1 1.0 CB C:GLN29 4.5 24.9 1.0 CB C:SER95 4.5 28.8 1.0 CA C:CYS24 4.6 28.4 1.0 CB C:GLN26 4.6 37.7 1.0 CA C:CYS90 4.6 25.9 1.0 CB C:GLN92 4.6 24.3 1.0 C C:GLN26 4.7 36.0 1.0 C C:CYS93 4.7 27.4 1.0 C C:CYS27 4.7 32.0 1.0 N C:GLY28 4.8 28.0 1.0 C C:GLN92 4.8 25.4 1.0 N C:GLY94 4.8 28.8 1.0 N C:GLN29 4.8 26.9 1.0 N C:SER95 4.9 27.8 1.0

C.Steinebach, A.Bricelj, A.Murgai, I.Sosic, L.Bischof, Y.L.D.Ng, C.Heim, S.Maiwald, M.Proj, R.Voget, F.Feller, J.Kosmrlj, V.Sapozhnikova, A.Schmidt, M.R.Zuleeg, P.Lemnitzer, P.Mertins, F.K.Hansen, M.Gutschow, J.Kronke, M.D.Hartmann. Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders For the Design of Protacs. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37902300
DOI: 10.1021/ACS.JMEDCHEM.3C00851