Zinc in PDB 8ou9: Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11E

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11E, PDB code: 8ou9 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)	47.49 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.328, 59.739, 88.305, 90, 90, 90
R / Rfree (%)	18.1 / 22.4

The binding sites of Zinc atom in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11E (pdb code 8ou9). 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 11E, PDB code: 8ou9:
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 11E


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 11E within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:23.8 occ:1.00 SG A:CYS93 2.3 24.1 1.0 SG A:CYS24 2.3 22.8 1.0 SG A:CYS90 2.4 23.6 1.0 SG A:CYS27 2.4 24.6 1.0 HB3 A:CYS24 3.0 21.5 1.0 HB3 A:CYS90 3.1 21.9 1.0 HB3 A:CYS93 3.1 22.7 1.0 CB A:CYS90 3.1 22.1 1.0 CB A:CYS24 3.1 21.7 1.0 HB2 A:CYS90 3.1 22.0 1.0 H A:CYS93 3.2 23.8 1.0 HB3 A:CYS27 3.3 23.5 1.0 CB A:CYS93 3.3 22.2 1.0 HB2 A:CYS24 3.3 21.5 1.0 HB3 A:GLN26 3.4 33.5 1.0 CB A:CYS27 3.5 22.8 1.0 H A:CYS27 3.6 26.3 1.0 HB3 A:SER95 3.8 30.9 0.5 N A:CYS93 3.8 23.2 1.0 HB3 A:GLN92 3.9 24.5 1.0 HB3 A:GLN29 3.9 21.2 1.0 HB2 A:SER95 3.9 30.4 0.5 N A:CYS27 4.0 24.3 1.0 CA A:CYS93 4.0 22.8 1.0 HB2 A:CYS93 4.1 22.7 1.0 H A:SER95 4.2 27.8 1.0 HB2 A:CYS27 4.2 23.4 1.0 H A:GLN29 4.2 22.6 1.0 HB2 A:GLN29 4.2 21.3 1.0 CA A:CYS27 4.3 24.1 1.0 CB A:GLN26 4.4 31.3 1.0 H A:GLN26 4.4 25.6 1.0 HD11 A:LEU97 4.4 26.6 1.0 H A:GLY28 4.5 24.9 1.0 H A:GLY94 4.5 25.2 1.0 H A:GLN92 4.5 25.1 1.0 CB A:GLN29 4.5 21.0 1.0 CA A:CYS24 4.6 20.2 1.0 HE21 A:GLN92 4.6 24.7 1.0 CA A:CYS90 4.6 20.4 1.0 CB A:SER95 4.7 31.1 0.5 HB2 A:SER95 4.7 30.9 0.5 C A:GLN26 4.7 34.2 1.0 C A:CYS93 4.8 26.0 1.0 CB A:GLN92 4.8 25.1 1.0 HD23 A:LEU97 4.8 27.4 1.0 CB A:SER95 4.8 30.3 0.5 HA A:CYS93 4.9 23.4 1.0 HB2 A:GLN26 4.9 33.7 1.0 HG2 A:GLN92 4.9 24.9 1.0 HG2 A:GLN26 4.9 45.8 1.0 CA A:GLN26 4.9 26.4 1.0 N A:GLY94 4.9 25.1 1.0 C A:GLN92 4.9 26.0 1.0 N A:GLN26 4.9 25.2 1.0 N A:GLY28 4.9 24.5 1.0 C A:CYS27 5.0 26.6 1.0 HG3 A:GLN26 5.0 45.7 1.0 HA A:CYS90 5.0 20.9 1.0 HA A:CYS24 5.0 21.1 1.0

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


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 11E within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:28.8 occ:1.00 SG B:CYS90 2.3 26.3 1.0 SG B:CYS93 2.3 30.5 1.0 SG B:CYS27 2.3 29.4 1.0 SG B:CYS24 2.4 29.4 1.0 HB3 B:CYS93 3.0 32.1 1.0 HB3 B:CYS24 3.0 27.3 1.0 HB3 B:CYS90 3.0 26.7 1.0 CB B:CYS90 3.1 27.5 1.0 H B:CYS93 3.1 28.0 1.0 HB3 B:CYS27 3.1 30.5 1.0 CB B:CYS24 3.2 27.6 1.0 HB2 B:CYS90 3.2 26.7 1.0 CB B:CYS93 3.2 34.5 1.0 HB2 B:CYS24 3.2 27.3 1.0 CB B:CYS27 3.3 31.2 1.0 H B:CYS27 3.4 31.9 1.0 N B:CYS93 3.7 27.0 1.0 HB3 B:GLN92 3.7 30.9 1.0 HB2 B:GLN26 3.8 34.7 1.0 N B:CYS27 3.9 31.0 1.0 HB3 B:SER95 4.0 28.4 1.0 HB2 B:CYS93 4.0 32.2 1.0 CA B:CYS93 4.0 28.4 1.0 H B:GLN29 4.1 27.6 1.0 HB2 B:CYS27 4.1 30.5 1.0 CA B:CYS27 4.2 29.7 1.0 HB3 B:GLN29 4.2 34.0 1.0 H B:SER95 4.2 27.6 1.0 H B:GLY28 4.4 27.2 1.0 H B:GLY94 4.5 27.5 1.0 H B:GLN92 4.5 27.9 1.0 HB2 B:GLN29 4.5 34.0 1.0 HD11 B:LEU97 4.5 27.2 1.0 HB2 B:SER95 4.5 28.4 1.0 CA B:CYS90 4.6 24.9 1.0 H B:GLN26 4.6 33.0 1.0 CA B:CYS24 4.6 25.2 1.0 CB B:GLN92 4.6 30.1 1.0 CB B:GLN26 4.7 33.2 1.0 C B:GLN26 4.7 36.8 1.0 CB B:SER95 4.7 27.7 1.0 C B:GLN92 4.7 29.9 1.0 HE21 B:GLN92 4.8 30.8 1.0 C B:CYS27 4.8 30.9 1.0 C B:CYS93 4.8 30.5 1.0 HB3 B:GLN26 4.8 35.1 1.0 CB B:GLN29 4.8 33.6 1.0 HG2 B:GLN92 4.8 33.4 1.0 HA B:CYS93 4.8 29.6 1.0 N B:GLY28 4.8 26.5 1.0 HA B:CYS90 4.9 25.4 1.0 N B:GLY94 4.9 27.0 1.0 N B:GLN29 5.0 29.3 1.0 HD13 B:ILE31 5.0 25.2 1.0 HA B:CYS27 5.0 30.5 1.0

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


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 11E within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:30.7 occ:1.00 SG C:CYS27 2.3 33.1 1.0 SG C:CYS90 2.3 31.7 1.0 SG C:CYS93 2.3 35.5 1.0 SG C:CYS24 2.4 32.1 1.0 HB3 C:CYS24 3.0 34.9 1.0 CB C:CYS24 3.2 34.6 1.0 HB3 C:CYS90 3.2 31.2 1.0 CB C:CYS90 3.2 32.2 1.0 H C:CYS93 3.2 32.0 1.0 HB2 C:CYS90 3.2 31.2 1.0 HB3 C:CYS27 3.2 39.1 1.0 HB2 C:CYS24 3.3 34.9 1.0 HB3 C:CYS93 3.3 32.4 1.0 H C:CYS27 3.4 38.5 1.0 CB C:CYS27 3.4 41.4 1.0 CB C:CYS93 3.4 31.8 1.0 HB2 C:GLN26 3.5 43.0 1.0 HB3 C:GLN92 3.8 29.0 1.0 HB3 C:SER95 3.8 42.6 1.0 N C:CYS93 3.8 32.0 1.0 N C:CYS27 3.8 37.3 1.0 HB3 C:GLN29 3.9 28.5 1.0 HB2 C:GLN29 4.0 28.5 1.0 H C:SER95 4.1 36.5 1.0 H C:GLN29 4.1 28.9 1.0 CA C:CYS93 4.1 31.6 1.0 CA C:CYS27 4.1 38.9 1.0 HB2 C:CYS27 4.2 39.1 1.0 HB2 C:CYS93 4.2 32.4 1.0 H C:GLY28 4.3 33.5 1.0 H C:GLY94 4.3 31.0 1.0 H C:GLN92 4.4 30.4 1.0 H C:GLN26 4.5 37.1 1.0 CB C:GLN29 4.5 29.2 1.0 CB C:GLN26 4.5 41.8 1.0 HD11 C:LEU97 4.5 33.5 1.0 HG2 C:GLN92 4.6 27.3 1.0 CA C:CYS24 4.6 37.8 1.0 CA C:CYS90 4.6 28.6 1.0 CB C:GLN92 4.7 30.1 1.0 CB C:SER95 4.7 44.4 1.0 HE21 C:GLN92 4.7 29.1 1.0 C C:GLN26 4.7 41.8 1.0 C C:CYS27 4.7 34.7 1.0 N C:GLY28 4.8 32.7 1.0 C C:CYS93 4.8 34.1 1.0 C C:GLN92 4.8 32.6 1.0 N C:GLY94 4.8 29.0 1.0 HB2 C:SER95 4.8 42.6 1.0 HB3 C:GLN26 4.8 43.2 1.0 HD23 C:LEU97 4.9 30.5 1.0 N C:GLN29 4.9 29.0 1.0 N C:SER95 4.9 35.2 1.0 HA C:CYS93 5.0 32.1 1.0 HA C:CYS90 5.0 29.2 1.0 N C:GLN26 5.0 35.0 1.0 HA C:CYS27 5.0 38.3 1.0 N C:GLN92 5.0 30.6 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