Zinc in PDB 8ou6: Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11C

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11C, PDB code: 8ou6 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)	37.12 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.989, 59.126, 87.139, 90, 90, 90
R / Rfree (%)	18.4 / 22.5

The binding sites of Zinc atom in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11C (pdb code 8ou6). 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 11C, PDB code: 8ou6:
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 11C


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 11C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:36.0 occ:1.00 SG A:CYS93 2.3 39.0 1.0 SG A:CYS24 2.3 36.2 1.0 SG A:CYS27 2.3 36.1 1.0 SG A:CYS90 2.3 34.7 1.0 HB3 A:CYS24 3.0 31.6 1.0 CB A:CYS90 3.1 31.9 1.0 HB3 A:CYS90 3.1 32.4 1.0 H A:CYS93 3.1 34.9 1.0 HB2 A:CYS90 3.1 32.4 1.0 CB A:CYS24 3.1 31.0 1.0 HB3 A:CYS93 3.1 39.2 1.0 CB A:CYS93 3.3 40.6 1.0 HB2 A:CYS24 3.3 31.6 1.0 HB3 A:CYS27 3.4 37.1 1.0 CB A:CYS27 3.5 37.4 1.0 HB3 A:GLN26 3.6 50.9 0.5 HB3 A:GLN26 3.6 50.9 0.5 H A:CYS27 3.6 37.6 1.0 HB3 A:SER95 3.7 44.0 1.0 HB3 A:GLN29 3.7 35.0 1.0 HB3 A:GLN92 3.7 34.9 1.0 N A:CYS93 3.8 34.1 1.0 N A:CYS27 4.0 35.9 1.0 CA A:CYS93 4.1 36.5 1.0 HB2 A:CYS93 4.1 39.2 1.0 H A:GLN29 4.1 34.5 1.0 HB2 A:GLN29 4.1 35.0 1.0 HG3 A:GLN26 4.1 61.3 0.5 HG3 A:GLN26 4.1 61.3 0.5 H A:SER95 4.1 37.8 1.0 H A:GLN26 4.2 39.3 1.0 HB2 A:CYS27 4.3 37.1 1.0 CA A:CYS27 4.3 37.2 1.0 CB A:GLN26 4.4 49.6 0.5 CB A:GLN26 4.4 49.6 0.5 CB A:GLN29 4.4 35.1 1.0 HG2 A:GLN26 4.5 61.4 0.5 HG2 A:GLN26 4.5 61.4 0.5 HD11 A:LEU97 4.5 35.3 1.0 H A:GLY94 4.5 37.4 1.0 CA A:CYS90 4.6 31.6 1.0 HE21 A:GLN92 4.6 36.1 1.0 CA A:CYS24 4.6 29.8 1.0 H A:GLN92 4.6 36.2 1.0 CG A:GLN26 4.6 63.8 0.5 CG A:GLN26 4.6 63.8 0.5 CB A:SER95 4.6 43.9 1.0 H A:GLY28 4.6 32.5 1.0 C A:GLN26 4.6 42.5 1.0 CB A:GLN92 4.7 35.3 1.0 HB2 A:SER95 4.7 44.1 1.0 C A:CYS93 4.8 36.1 1.0 N A:GLN26 4.8 37.5 1.0 CA A:GLN26 4.8 43.9 0.5 CA A:GLN26 4.8 43.9 0.5 HG2 A:GLN92 4.9 34.9 1.0 HA A:CYS90 4.9 32.9 1.0 HD23 A:LEU97 4.9 33.9 1.0 C A:GLN92 4.9 35.1 1.0 HA A:CYS93 4.9 36.6 1.0 N A:GLY94 4.9 38.2 1.0 C A:CYS27 4.9 37.9 1.0 N A:GLN29 4.9 35.6 1.0 C A:CYS24 5.0 31.0 1.0 N A:SER95 5.0 36.8 1.0 N A:GLY28 5.0 31.7 1.0

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


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 11C within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:53.0 occ:1.00 SG B:CYS90 2.3 50.5 1.0 SG B:CYS24 2.3 49.0 1.0 SG B:CYS93 2.3 53.7 1.0 SG B:CYS27 2.3 55.4 1.0 HB3 B:CYS27 3.0 52.8 1.0 HB3 B:CYS90 3.0 46.4 1.0 CB B:CYS90 3.0 47.9 1.0 H B:CYS93 3.1 57.3 1.0 HB2 B:CYS90 3.1 46.4 1.0 HB3 B:CYS24 3.1 46.1 1.0 CB B:CYS24 3.2 48.2 1.0 CB B:CYS27 3.2 52.5 1.0 HB3 B:CYS93 3.3 55.4 1.0 HB2 B:CYS24 3.3 46.1 1.0 CB B:CYS93 3.4 56.5 1.0 H B:CYS27 3.5 57.1 1.0 HB3 B:GLN92 3.6 55.8 1.0 HB2 B:GLN26 3.7 59.7 1.0 N B:CYS93 3.7 57.9 1.0 N B:CYS27 3.9 57.6 1.0 HB3 B:SER95 3.9 50.2 1.0 HB2 B:CYS27 4.0 52.8 1.0 CA B:CYS27 4.1 51.3 1.0 CA B:CYS93 4.1 54.2 1.0 H B:GLN29 4.1 46.0 1.0 HB3 B:GLN29 4.2 54.6 1.0 HB2 B:CYS93 4.2 55.4 1.0 H B:SER95 4.3 48.4 1.0 H B:GLN92 4.5 49.1 1.0 HD11 B:LEU97 4.5 43.7 1.0 H B:GLY94 4.5 51.6 1.0 CA B:CYS90 4.5 40.3 1.0 H B:GLY28 4.5 47.6 1.0 H B:GLN26 4.5 55.8 1.0 CB B:GLN92 4.6 57.0 1.0 HB2 B:GLN29 4.6 54.6 1.0 CA B:CYS24 4.6 39.7 1.0 CB B:GLN26 4.6 55.9 1.0 C B:GLN26 4.7 62.7 1.0 C B:CYS27 4.7 52.5 1.0 C B:GLN92 4.8 59.6 1.0 C B:CYS93 4.8 55.4 1.0 HA B:CYS90 4.8 41.7 1.0 HG2 B:GLN92 4.8 57.7 1.0 CB B:SER95 4.8 48.1 1.0 CB B:GLN29 4.8 55.0 1.0 HB3 B:GLN26 4.9 59.8 1.0 HE21 B:GLN92 4.9 56.2 1.0 N B:GLY28 4.9 45.1 1.0 N B:GLY94 4.9 51.7 1.0 HA B:CYS93 4.9 55.6 1.0 HA B:CYS27 4.9 53.0 1.0 HB2 B:SER95 5.0 50.2 1.0 N B:GLN29 5.0 45.8 1.0 C B:CYS90 5.0 44.6 1.0

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


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 11C within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:50.3 occ:1.00 SG C:CYS93 2.3 52.8 1.0 SG C:CYS27 2.4 49.5 1.0 SG C:CYS90 2.4 51.3 1.0 SG C:CYS24 2.4 55.9 1.0 H C:CYS93 3.0 49.5 1.0 HB3 C:CYS24 3.0 57.1 1.0 HB3 C:CYS27 3.1 52.1 1.0 HB3 C:CYS93 3.1 54.9 1.0 HB3 C:CYS90 3.1 55.8 1.0 CB C:CYS24 3.2 58.6 1.0 CB C:CYS90 3.2 56.1 1.0 HB2 C:CYS90 3.3 55.8 1.0 CB C:CYS93 3.3 57.5 1.0 CB C:CYS27 3.3 53.6 1.0 H C:CYS27 3.3 55.4 1.0 HB2 C:CYS24 3.4 57.1 1.0 HB3 C:GLN92 3.6 45.4 1.0 N C:CYS93 3.7 50.7 1.0 N C:CYS27 3.8 54.9 1.0 HB3 C:GLN29 3.8 45.7 1.0 HB2 C:GLN26 3.8 61.3 1.0 HB2 C:SER95 3.8 74.0 1.0 CA C:CYS93 4.0 50.8 1.0 H C:SER95 4.1 70.0 1.0 CA C:CYS27 4.1 50.7 1.0 H C:GLN29 4.1 47.1 1.0 HB2 C:CYS27 4.1 52.1 1.0 HB2 C:CYS93 4.1 54.9 1.0 HB2 C:GLN29 4.1 45.7 1.0 H C:GLY94 4.2 63.5 1.0 H C:GLY28 4.2 47.8 1.0 H C:GLN92 4.4 47.8 1.0 H C:GLN26 4.4 54.9 1.0 CB C:GLN29 4.5 45.1 1.0 HE21 C:GLN92 4.6 41.9 1.0 CB C:GLN92 4.6 46.6 1.0 CB C:GLN26 4.6 62.3 1.0 HB3 C:GLN26 4.6 61.4 1.0 CA C:CYS24 4.6 54.4 1.0 C C:GLN26 4.6 62.2 1.0 C C:CYS93 4.7 58.2 1.0 N C:GLY94 4.7 64.6 1.0 CA C:CYS90 4.7 59.0 1.0 CB C:SER95 4.7 70.8 1.0 N C:GLY28 4.7 45.9 1.0 C C:GLN92 4.7 45.3 1.0 C C:CYS27 4.7 51.0 1.0 HG2 C:GLN92 4.8 44.2 1.0 HA C:CYS93 4.9 53.2 1.0 OG C:SER95 4.9 83.5 1.0 N C:SER95 4.9 68.0 1.0 N C:GLN29 4.9 48.1 1.0 HA C:CYS27 4.9 52.2 1.0 N C:GLN26 4.9 53.3 1.0 CA C:GLN26 5.0 53.6 1.0 N C:GLN92 5.0 46.8 1.0 CA C:GLN92 5.0 43.7 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