Zinc in PDB 8ou5: Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11B

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11B, PDB code: 8ou5 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)	49.42 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.839, 59.572, 88.484, 90, 90, 90
R / Rfree (%)	20.5 / 25.3

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

Fluorine

(F)

6 atoms

The binding sites of Zinc atom in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11B (pdb code 8ou5). 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 11B, PDB code: 8ou5:
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 11B


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 11B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:44.6 occ:1.00 SG A:CYS93 2.3 45.5 1.0 SG A:CYS90 2.3 40.4 1.0 SG A:CYS24 2.3 41.3 1.0 SG A:CYS27 2.4 47.6 1.0 HB3 A:CYS24 3.0 41.4 1.0 HB3 A:CYS93 3.1 45.1 1.0 HB3 A:CYS90 3.1 40.5 1.0 CB A:CYS24 3.1 41.3 1.0 H A:CYS93 3.2 42.1 1.0 CB A:CYS90 3.2 40.0 1.0 HB3 A:CYS27 3.2 47.5 1.0 HB2 A:CYS90 3.2 39.3 1.0 CB A:CYS93 3.3 44.7 1.0 HB2 A:CYS24 3.3 40.5 1.0 H A:CYS27 3.4 46.9 1.0 CB A:CYS27 3.4 46.9 1.0 HB3 A:GLN26 3.4 57.6 1.0 HB3 A:GLN92 3.7 40.1 1.0 HB3 A:SER95 3.7 50.9 1.0 N A:CYS93 3.8 43.3 1.0 HB3 A:GLN29 3.8 44.7 1.0 N A:CYS27 3.9 47.7 1.0 HB2 A:CYS93 4.0 46.3 1.0 CA A:CYS93 4.1 45.6 1.0 H A:GLN29 4.1 44.6 1.0 H A:SER95 4.2 49.0 1.0 HB2 A:CYS27 4.2 48.0 1.0 CA A:CYS27 4.2 46.8 1.0 H A:GLY28 4.2 43.9 1.0 H A:GLN26 4.3 47.7 1.0 HB2 A:GLN29 4.3 45.8 1.0 CB A:GLN26 4.4 58.6 1.0 H A:GLY94 4.4 45.9 1.0 HE21 A:GLN92 4.4 42.2 1.0 H A:GLN92 4.6 39.7 1.0 CB A:GLN29 4.6 45.2 1.0 CA A:CYS24 4.6 40.3 1.0 HD11 A:LEU97 4.6 44.4 1.0 CA A:CYS90 4.6 38.9 1.0 CB A:SER95 4.7 51.4 1.0 CB A:GLN92 4.7 40.8 1.0 C A:GLN26 4.7 49.9 1.0 HG3 A:GLN26 4.8 67.0 1.0 HB2 A:SER95 4.8 52.6 1.0 C A:CYS93 4.8 46.9 1.0 N A:GLY28 4.8 44.2 1.0 HG2 A:GLN26 4.8 67.1 1.0 N A:GLY94 4.9 46.6 1.0 C A:CYS27 4.9 46.1 1.0 C A:GLN92 4.9 42.3 1.0 HA A:CYS93 4.9 46.6 1.0 N A:GLN26 4.9 48.8 1.0 HD23 A:LEU97 4.9 43.6 1.0 CA A:GLN26 4.9 51.9 1.0 HB2 A:GLN26 4.9 58.7 1.0 CG A:GLN26 4.9 67.6 1.0 N A:GLN29 4.9 45.1 1.0 HA A:CYS90 5.0 38.7 1.0 C A:CYS24 5.0 41.5 1.0 HA A:CYS24 5.0 40.4 1.0

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


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 11B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:52.6 occ:1.00 SG B:CYS27 2.3 52.9 1.0 SG B:CYS90 2.3 51.9 1.0 SG B:CYS93 2.3 49.3 1.0 SG B:CYS24 2.5 50.4 1.0 HB3 B:CYS93 3.0 53.3 1.0 H B:CYS93 3.0 51.8 1.0 HB3 B:CYS24 3.0 51.5 1.0 HB3 B:CYS27 3.1 55.6 1.0 CB B:CYS93 3.2 52.9 1.0 CB B:CYS24 3.2 50.5 1.0 HB3 B:CYS90 3.2 51.1 1.0 CB B:CYS90 3.2 50.1 1.0 CB B:CYS27 3.3 55.3 1.0 HB2 B:CYS90 3.3 49.1 1.0 HB2 B:CYS24 3.3 49.4 1.0 H B:CYS27 3.4 54.7 1.0 HB3 B:GLN92 3.5 57.8 1.0 N B:CYS93 3.6 52.9 1.0 N B:CYS27 3.9 56.8 1.0 CA B:CYS93 4.0 53.9 1.0 HB3 B:SER95 4.0 52.4 1.0 HB2 B:CYS93 4.0 54.5 1.0 H B:GLN29 4.0 53.5 1.0 HB2 B:CYS27 4.1 57.1 1.0 HB3 B:GLN29 4.1 56.0 1.0 CA B:CYS27 4.1 56.1 1.0 H B:GLY28 4.2 51.6 1.0 H B:SER95 4.3 51.8 1.0 H B:GLY94 4.4 50.6 1.0 H B:GLN92 4.4 51.9 1.0 CB B:GLN92 4.4 58.9 1.0 H B:GLN26 4.5 55.8 1.0 HB2 B:GLN29 4.5 58.4 1.0 CB B:GLN26 4.6 58.4 1.0 HD11 B:LEU97 4.6 44.9 1.0 CA B:CYS24 4.7 50.1 1.0 CA B:CYS90 4.7 48.8 1.0 C B:GLN92 4.7 56.9 1.0 N B:GLY28 4.7 52.8 1.0 C B:CYS93 4.7 54.0 1.0 C B:CYS27 4.8 54.1 1.0 HA B:CYS93 4.8 56.0 1.0 CB B:GLN29 4.8 57.2 1.0 HG2 B:GLN92 4.8 63.9 1.0 C B:GLN26 4.8 58.7 1.0 HE21 B:GLN92 4.8 66.7 1.0 N B:GLY94 4.8 51.8 1.0 CB B:SER95 4.9 52.6 1.0 HB2 B:SER95 4.9 54.5 1.0 HB2 B:GLN92 4.9 58.0 1.0 N B:GLN29 4.9 53.6 1.0 CA B:GLN92 4.9 57.1 1.0 HA B:CYS27 5.0 58.1 1.0 HA B:CYS90 5.0 47.5 1.0

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


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 11B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:64.8 occ:1.00 SG C:CYS93 2.2 64.5 1.0 SG C:CYS90 2.3 65.9 1.0 SG C:CYS27 2.4 67.0 1.0 SG C:CYS24 2.4 66.1 1.0 HB3 C:CYS93 3.0 64.6 1.0 H C:CYS93 3.1 63.7 1.0 HB3 C:CYS24 3.1 66.5 1.0 HB3 C:CYS90 3.1 66.9 1.0 CB C:CYS90 3.2 66.4 1.0 HB3 C:CYS27 3.2 70.9 1.0 CB C:CYS93 3.2 65.1 1.0 HB2 C:CYS90 3.2 67.2 1.0 CB C:CYS24 3.3 67.0 1.0 CB C:CYS27 3.4 71.1 1.0 HB2 C:CYS24 3.4 66.3 1.0 H C:CYS27 3.4 74.1 1.0 HB2 C:GLN26 3.4 77.6 1.0 HB3 C:GLN92 3.6 58.4 1.0 N C:CYS93 3.7 64.0 1.0 HB3 C:SER95 3.7 76.0 1.0 HB3 C:GLN29 3.8 63.3 1.0 N C:CYS27 3.9 74.2 1.0 CA C:CYS93 4.0 65.3 1.0 HB2 C:CYS93 4.0 66.1 1.0 H C:GLN29 4.1 64.1 1.0 H C:SER95 4.1 72.9 1.0 HB2 C:CYS27 4.1 70.0 1.0 CA C:CYS27 4.2 72.3 1.0 H C:GLY28 4.2 69.5 1.0 HB2 C:GLN29 4.3 62.5 1.0 HE21 C:GLN92 4.3 55.9 1.0 H C:GLY94 4.3 67.4 1.0 H C:GLN26 4.4 77.8 1.0 CB C:GLN26 4.4 79.0 1.0 H C:GLN92 4.5 59.8 1.0 CB C:GLN29 4.5 62.7 1.0 CB C:GLN92 4.6 57.9 1.0 CA C:CYS90 4.6 65.9 1.0 CB C:SER95 4.6 77.3 1.0 HD11 C:LEU97 4.6 73.2 1.0 HB2 C:SER95 4.7 77.8 1.0 C C:CYS93 4.7 67.6 1.0 CA C:CYS24 4.7 70.1 1.0 C C:GLN92 4.8 62.1 1.0 N C:GLY94 4.8 68.3 1.0 N C:GLY28 4.8 69.1 1.0 C C:GLN26 4.8 78.2 1.0 HA C:CYS93 4.8 65.3 1.0 HB3 C:GLN26 4.8 79.6 1.0 C C:CYS27 4.8 70.5 1.0 N C:SER95 4.9 73.8 1.0 HG2 C:GLN92 4.9 56.8 1.0 HA C:CYS90 4.9 65.6 1.0 N C:GLN26 5.0 78.7 1.0 N C:GLN29 5.0 63.8 1.0 CA C:GLN26 5.0 79.3 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