Zinc in PDB 8oua: Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F, PDB code: 8oua was solved by C.Heim, L.Bischof, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.30 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.422, 59.472, 88.147, 90, 90, 90
R / Rfree (%)	18.4 / 23.8

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Zinc atom in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F (pdb code 8oua). 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 11F, PDB code: 8oua:
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 11F


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 11F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:27.6 occ:1.00 SG A:CYS24 2.3 26.4 1.0 SG A:CYS93 2.3 27.4 1.0 SG A:CYS27 2.3 30.1 1.0 SG A:CYS90 2.3 27.6 1.0 HB3 A:CYS24 3.0 24.4 1.0 HB3 A:CYS93 3.1 30.5 1.0 CB A:CYS90 3.1 23.5 1.0 CB A:CYS24 3.1 24.0 1.0 HB2 A:CYS90 3.1 23.2 1.0 H A:CYS93 3.1 32.3 1.0 HB3 A:CYS90 3.2 23.2 1.0 CB A:CYS93 3.3 31.8 1.0 HB2 A:CYS24 3.3 24.4 1.0 HB3 A:CYS27 3.3 28.0 1.0 HB2 A:GLN26 3.4 40.8 1.0 CB A:CYS27 3.5 27.2 1.0 H A:CYS27 3.5 29.0 1.0 HB3 A:SER95 3.8 31.2 0.5 N A:CYS93 3.8 32.9 1.0 HB3 A:GLN29 3.8 29.8 1.0 HB3 A:GLN92 3.8 29.4 1.0 N A:CYS27 3.9 26.2 1.0 HB2 A:SER95 4.0 35.2 0.5 CA A:CYS93 4.0 30.1 1.0 HB2 A:CYS93 4.1 30.5 1.0 H A:GLN29 4.2 28.0 1.0 HB2 A:CYS27 4.2 28.0 1.0 H A:SER95 4.2 29.8 1.0 CA A:CYS27 4.2 28.4 1.0 HB2 A:GLN29 4.3 29.8 1.0 CB A:GLN26 4.4 39.4 1.0 H A:GLN26 4.4 30.0 1.0 HD11 A:LEU97 4.5 30.8 1.0 CB A:GLN29 4.5 31.7 1.0 H A:GLN92 4.5 30.9 1.0 CA A:CYS24 4.5 24.1 1.0 H A:GLY28 4.5 30.2 1.0 HE21 A:GLN92 4.6 27.8 1.0 CA A:CYS90 4.6 19.4 1.0 H A:GLY94 4.6 28.2 1.0 HB3 A:GLN26 4.6 41.3 1.0 CB A:SER95 4.7 31.4 0.5 C A:GLN26 4.7 36.6 1.0 HB2 A:SER95 4.7 31.2 0.5 C A:CYS93 4.7 28.3 1.0 CB A:GLN92 4.7 29.3 1.0 HD23 A:LEU97 4.8 28.8 1.0 HA A:CYS93 4.8 30.6 1.0 CB A:SER95 4.8 35.4 0.5 HG2 A:GLN92 4.9 28.9 1.0 C A:GLN92 4.9 33.1 1.0 HA A:CYS90 4.9 22.0 1.0 CA A:GLN26 4.9 34.6 1.0 C A:CYS27 4.9 30.9 1.0 N A:GLN26 4.9 29.1 1.0 N A:GLY94 4.9 27.8 1.0 N A:GLY28 4.9 30.0 1.0 HA A:CYS24 4.9 25.7 1.0 OG A:SER95 4.9 35.7 0.5 C A:CYS24 5.0 32.0 1.0 N A:GLN29 5.0 28.3 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F


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 11F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:36.3 occ:1.00 SG B:CYS90 2.3 34.6 1.0 SG B:CYS93 2.3 35.9 1.0 SG B:CYS27 2.3 37.5 1.0 SG B:CYS24 2.4 34.5 1.0 HB3 B:CYS93 3.0 35.1 1.0 HB3 B:CYS90 3.0 33.5 1.0 CB B:CYS90 3.1 34.1 1.0 HB3 B:CYS24 3.1 35.9 1.0 H B:CYS93 3.1 33.1 1.0 HB2 B:CYS90 3.2 33.5 1.0 HB3 B:CYS27 3.2 36.8 1.0 CB B:CYS24 3.2 36.5 1.0 CB B:CYS93 3.2 36.6 1.0 H B:CYS27 3.3 40.9 1.0 HB2 B:CYS24 3.3 36.0 1.0 CB B:CYS27 3.4 36.5 1.0 HB2 B:GLN26 3.7 34.4 0.5 HB3 B:GLN29 3.7 41.6 1.0 N B:CYS93 3.7 31.8 1.0 HB3 B:GLN92 3.7 35.9 1.0 N B:CYS27 3.8 42.0 1.0 HB3 B:GLN26 3.9 37.0 0.5 HB3 B:SER95 3.9 37.0 1.0 CA B:CYS93 4.0 31.2 1.0 HB2 B:CYS93 4.0 35.1 1.0 HG2 B:GLN26 4.1 37.2 0.5 CA B:CYS27 4.1 36.9 1.0 HB2 B:CYS27 4.1 36.8 1.0 H B:SER95 4.2 33.0 1.0 H B:GLN29 4.2 30.9 1.0 H B:GLN92 4.4 35.1 1.0 HD11 B:LEU97 4.5 31.8 1.0 H B:GLY94 4.5 32.8 1.0 CA B:CYS90 4.5 31.4 1.0 H B:GLY28 4.6 33.4 1.0 H B:GLN26 4.6 36.5 1.0 CB B:GLN29 4.6 41.1 1.0 CB B:GLN26 4.6 34.6 0.5 CB B:GLN92 4.6 36.1 1.0 CA B:CYS24 4.7 35.9 1.0 CB B:GLN26 4.7 37.1 0.5 C B:CYS93 4.7 37.2 1.0 HB2 B:GLN29 4.7 41.8 1.0 C B:GLN92 4.7 38.5 1.0 HB2 B:SER95 4.7 37.0 1.0 HG2 B:GLN92 4.7 37.2 1.0 C B:GLN26 4.8 43.0 1.0 CB B:SER95 4.8 37.0 1.0 HG2 B:GLN29 4.8 51.0 1.0 HE21 B:GLN92 4.8 37.2 1.0 C B:CYS27 4.8 40.4 1.0 HA B:CYS93 4.8 33.4 1.0 CG B:GLN26 4.8 37.2 0.5 N B:GLY94 4.9 31.0 1.0 HA B:CYS90 4.9 31.6 1.0 N B:GLY28 4.9 31.5 1.0 HA B:CYS27 5.0 38.4 1.0 HD13 B:ILE31 5.0 29.0 1.0 HB3 B:GLN26 5.0 34.4 0.5

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F


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 11F within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:38.8 occ:1.00 SG C:CYS93 2.3 40.9 1.0 SG C:CYS27 2.4 39.7 1.0 SG C:CYS24 2.4 41.7 1.0 SG C:CYS90 2.4 39.2 1.0 HB3 C:CYS90 3.1 43.9 1.0 H C:CYS93 3.1 38.6 1.0 HB3 C:CYS24 3.1 40.8 1.0 CB C:CYS90 3.1 45.2 1.0 CB C:CYS24 3.2 39.5 1.0 HB3 C:CYS27 3.2 49.4 1.0 HB2 C:CYS90 3.2 43.9 1.0 HB2 C:CYS24 3.3 40.8 1.0 H C:CYS27 3.3 50.6 1.0 HB3 C:CYS93 3.4 42.3 1.0 CB C:CYS27 3.4 53.4 1.0 CB C:CYS93 3.4 44.3 1.0 HB2 C:GLN26 3.4 54.8 1.0 HB3 C:SER95 3.7 52.8 1.0 N C:CYS93 3.7 38.3 1.0 HB3 C:GLN92 3.8 32.3 1.0 N C:CYS27 3.8 50.0 1.0 HB3 C:GLN29 3.8 35.0 1.0 H C:SER95 4.0 47.7 1.0 H C:GLN29 4.1 38.1 1.0 CA C:CYS93 4.1 38.9 1.0 CA C:CYS27 4.1 48.7 1.0 HB2 C:GLN29 4.2 35.0 1.0 HB2 C:CYS27 4.2 49.4 1.0 HB2 C:CYS93 4.2 42.3 1.0 H C:GLY28 4.3 39.1 1.0 H C:GLN92 4.3 34.9 1.0 CB C:GLN26 4.4 55.0 1.0 H C:GLY94 4.5 40.3 1.0 CB C:GLN29 4.5 33.4 1.0 H C:GLN26 4.5 44.8 1.0 HE21 C:GLN92 4.5 32.0 1.0 HD11 C:LEU97 4.6 43.6 1.0 CA C:CYS90 4.6 44.8 1.0 CB C:SER95 4.6 54.3 1.0 HG2 C:GLN92 4.6 32.0 1.0 CA C:CYS24 4.6 43.2 1.0 CB C:GLN92 4.7 32.5 1.0 C C:CYS93 4.7 42.1 1.0 C C:GLN26 4.7 55.2 1.0 C C:CYS27 4.7 42.4 1.0 C C:GLN92 4.8 39.4 1.0 N C:GLY28 4.8 37.2 1.0 N C:GLY94 4.8 37.7 1.0 HB2 C:SER95 4.8 52.9 1.0 N C:SER95 4.8 46.8 1.0 HD23 C:LEU97 4.8 42.1 1.0 HB3 C:GLN26 4.9 55.0 1.0 N C:GLN29 4.9 40.6 1.0 HA C:CYS93 5.0 40.3 1.0 N C:GLN92 5.0 34.6 1.0 HG3 C:GLN26 5.0 64.9 1.0 HA C:CYS27 5.0 48.6 1.0 CA C:GLN26 5.0 46.1 1.0 HA C:CYS90 5.0 43.5 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