Zinc in PDB 8ou7: Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11D

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11D, PDB code: 8ou7 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)	47.55 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.409, 59.548, 88.413, 90, 90, 90
R / Rfree (%)	17.6 / 22.4

The binding sites of Zinc atom in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11D (pdb code 8ou7). 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 11D, PDB code: 8ou7:
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 11D


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 11D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:27.6 occ:1.00 HG A:CYS90 1.2 26.6 0.0 HG A:CYS24 1.2 27.2 0.0 SG A:CYS93 2.3 28.8 1.0 SG A:CYS24 2.3 27.4 1.0 SG A:CYS27 2.3 27.7 1.0 SG A:CYS90 2.4 26.7 1.0 HG A:CYS27 2.4 27.5 0.0 HG A:CYS93 2.5 28.7 0.0 HB3 A:CYS24 3.0 26.2 1.0 HB3 A:CYS90 3.1 24.8 1.0 CB A:CYS90 3.1 24.9 1.0 H A:CYS93 3.1 29.3 1.0 CB A:CYS24 3.1 26.9 1.0 HB2 A:CYS90 3.2 24.8 1.0 HB3 A:CYS93 3.2 27.8 1.0 HB2 A:CYS24 3.3 26.2 1.0 CB A:CYS93 3.3 28.1 1.0 HB3 A:CYS27 3.4 29.4 1.0 HB2 A:GLN26 3.5 34.0 1.0 CB A:CYS27 3.5 29.7 1.0 H A:CYS27 3.6 30.6 1.0 HB3 A:GLN92 3.8 28.8 1.0 N A:CYS93 3.8 30.1 1.0 HB3 A:SER95 3.8 33.1 0.5 HB3 A:GLN29 3.9 27.0 1.0 N A:CYS27 4.0 28.6 1.0 HB2 A:SER95 4.0 33.7 0.5 CA A:CYS93 4.0 26.1 1.0 HB2 A:CYS93 4.1 27.8 1.0 H A:GLN29 4.2 26.8 1.0 HB2 A:GLN29 4.2 27.1 1.0 H A:SER95 4.2 29.9 1.0 HB2 A:CYS27 4.3 29.4 1.0 CA A:CYS27 4.3 29.9 1.0 HG A:SER95 4.3 32.7 0.0 H A:GLN26 4.4 27.4 1.0 CB A:GLN26 4.5 32.7 1.0 HD11 A:LEU97 4.5 29.9 1.0 HB2 A:SER95 4.5 33.1 0.5 HE21 A:GLN92 4.5 28.1 1.0 CB A:GLN29 4.5 26.5 1.0 H A:GLY28 4.6 28.6 1.0 CA A:CYS24 4.6 23.9 1.0 H A:GLY94 4.6 27.8 1.0 CA A:CYS90 4.6 23.0 1.0 H A:GLN92 4.6 28.6 1.0 CB A:SER95 4.6 33.4 0.5 C A:GLN26 4.7 36.9 1.0 CB A:GLN92 4.7 29.6 1.0 C A:CYS93 4.8 29.8 1.0 HB3 A:GLN26 4.8 34.0 1.0 HA A:CYS93 4.8 27.9 1.0 HG2 A:GLN92 4.9 28.6 1.0 CB A:SER95 4.9 34.6 0.5 HD23 A:LEU97 4.9 31.0 1.0 C A:CYS27 4.9 32.3 1.0 C A:GLN92 4.9 30.9 1.0 CA A:GLN26 4.9 28.5 1.0 HA A:CYS90 4.9 23.7 1.0 N A:GLN26 4.9 27.4 1.0 N A:GLY94 4.9 27.4 1.0 N A:GLY28 5.0 27.1 1.0 OG A:SER95 5.0 32.7 0.5 C A:CYS24 5.0 26.7 1.0

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


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 11D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:33.1 occ:1.00 HG B:CYS90 1.1 30.3 0.0 HG B:CYS24 1.2 30.8 0.0 SG B:CYS90 2.3 30.5 1.0 SG B:CYS93 2.3 33.7 1.0 SG B:CYS27 2.4 34.9 1.0 SG B:CYS24 2.4 31.1 1.0 HG B:CYS93 2.5 33.2 0.0 HG B:CYS27 2.5 34.6 0.0 HB3 B:CYS93 3.0 35.0 1.0 HB3 B:CYS90 3.0 29.7 1.0 CB B:CYS90 3.1 30.9 1.0 HB3 B:CYS24 3.1 32.0 1.0 HB2 B:CYS90 3.1 29.7 1.0 HB3 B:CYS27 3.1 35.3 1.0 CB B:CYS24 3.2 33.1 1.0 CB B:CYS93 3.2 37.4 1.0 H B:CYS93 3.3 32.5 1.0 HB2 B:CYS24 3.3 32.0 1.0 H B:CYS27 3.3 38.1 1.0 CB B:CYS27 3.4 35.7 1.0 HB2 B:GLN26 3.8 39.0 1.0 N B:CYS27 3.8 37.7 1.0 N B:CYS93 3.8 31.9 1.0 HB3 B:GLN92 3.9 35.2 1.0 HB3 B:SER95 3.9 32.2 1.0 HB2 B:CYS93 4.0 35.0 1.0 CA B:CYS93 4.1 30.8 1.0 H B:GLN29 4.1 30.6 1.0 HB2 B:CYS27 4.1 35.3 1.0 CA B:CYS27 4.2 34.6 1.0 H B:SER95 4.2 30.6 1.0 HB3 B:GLN29 4.2 37.5 1.0 HD11 B:LEU97 4.4 30.0 1.0 H B:GLN92 4.5 31.7 1.0 HB2 B:GLN29 4.5 37.5 1.0 H B:GLY28 4.5 34.4 1.0 H B:GLN26 4.5 36.8 1.0 HB2 B:SER95 4.5 32.2 1.0 CA B:CYS90 4.6 26.4 1.0 H B:GLY94 4.6 32.2 1.0 CA B:CYS24 4.6 30.3 1.0 CB B:GLN26 4.7 36.2 1.0 CB B:SER95 4.7 31.2 1.0 HG2 B:GLN92 4.7 35.9 1.0 C B:GLN26 4.7 43.0 1.0 CB B:GLN92 4.8 35.4 1.0 C B:CYS93 4.8 35.7 1.0 HE21 B:GLN92 4.8 32.2 1.0 C B:GLN92 4.8 35.8 1.0 C B:CYS27 4.8 38.8 1.0 CB B:GLN29 4.8 35.6 1.0 HA B:CYS93 4.9 33.1 1.0 HA B:CYS90 4.9 27.8 1.0 N B:GLY28 4.9 33.0 1.0 N B:GLY94 4.9 31.0 1.0 HB3 B:GLN26 4.9 39.1 1.0 HE21 B:GLN29 5.0 47.4 1.0 HA B:CYS27 5.0 36.2 1.0 N B:GLN29 5.0 31.0 1.0

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


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 11D within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:35.4 occ:1.00 HG C:CYS90 1.2 34.3 0.0 HG C:CYS24 1.2 37.0 0.0 SG C:CYS93 2.3 38.5 1.0 SG C:CYS27 2.3 36.1 1.0 SG C:CYS90 2.4 34.6 1.0 SG C:CYS24 2.4 37.3 1.0 HG C:CYS27 2.5 35.5 0.0 HG C:CYS93 2.5 38.1 0.0 HB3 C:CYS24 3.1 36.8 1.0 HB3 C:CYS90 3.1 34.8 1.0 CB C:CYS24 3.1 36.1 1.0 CB C:CYS90 3.2 34.5 1.0 HB3 C:CYS27 3.2 43.2 1.0 H C:CYS93 3.2 34.9 1.0 HB2 C:CYS24 3.2 36.8 1.0 HB3 C:CYS93 3.2 37.9 1.0 HB2 C:CYS90 3.2 34.8 1.0 CB C:CYS93 3.4 38.2 1.0 CB C:CYS27 3.4 44.8 1.0 H C:CYS27 3.4 51.2 1.0 HB2 C:GLN26 3.6 50.4 1.0 HB3 C:GLN92 3.7 29.8 1.0 HB3 C:SER95 3.7 48.6 1.0 N C:CYS93 3.8 34.4 1.0 HB3 C:GLN29 3.8 32.5 1.0 N C:CYS27 3.9 51.8 1.0 H C:GLN29 4.0 35.5 1.0 H C:SER95 4.0 41.9 1.0 CA C:CYS93 4.1 36.5 1.0 CA C:CYS27 4.1 45.4 1.0 HB2 C:CYS27 4.1 43.2 1.0 HB2 C:CYS93 4.1 37.9 1.0 HB2 C:GLN29 4.2 32.6 1.0 H C:GLN92 4.3 32.7 1.0 H C:GLY28 4.4 38.5 1.0 H C:GLY94 4.4 37.4 1.0 CB C:GLN29 4.5 30.6 1.0 H C:GLN26 4.5 44.6 1.0 HD11 C:LEU97 4.5 39.1 1.0 CB C:GLN26 4.6 47.7 1.0 CA C:CYS24 4.6 38.0 1.0 CA C:CYS90 4.6 35.6 1.0 CB C:GLN92 4.6 29.9 1.0 HE21 C:GLN92 4.7 33.2 1.0 CB C:SER95 4.7 49.5 1.0 C C:GLN26 4.7 57.4 1.0 C C:CYS27 4.7 42.0 1.0 C C:CYS93 4.8 43.8 1.0 HD23 C:LEU97 4.8 38.5 1.0 HG2 C:GLN92 4.8 30.6 1.0 N C:GLY94 4.8 33.2 1.0 N C:GLY28 4.8 36.3 1.0 C C:GLN92 4.8 34.7 1.0 HB2 C:SER95 4.8 48.6 1.0 N C:SER95 4.9 42.2 1.0 N C:GLN29 4.9 35.4 1.0 HA C:CYS93 5.0 37.6 1.0 HA C:CYS24 5.0 37.9 1.0 HA C:CYS90 5.0 34.4 1.0 N C:GLN92 5.0 31.9 1.0 HA C:CYS27 5.0 45.9 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