Zinc in PDB 8ou4: Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11A

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11A, PDB code: 8ou4 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)	47.58 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.511, 59.542, 88.185, 90, 90, 90
R / Rfree (%)	22.2 / 26.9

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

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11A (pdb code 8ou4). 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 11A, PDB code: 8ou4:
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 11A


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:41.9 occ:1.00 SG A:CYS93 2.2 41.6 1.0 SG A:CYS27 2.3 44.7 1.0 SG A:CYS24 2.3 38.5 1.0 SG A:CYS90 2.4 38.8 1.0 HB3 A:CYS24 3.0 37.3 1.0 HB3 A:CYS93 3.1 42.4 1.0 H A:CYS93 3.1 40.6 1.0 HB3 A:CYS90 3.2 38.6 1.0 CB A:CYS24 3.2 36.7 1.0 HB3 A:CYS27 3.2 44.5 1.0 CB A:CYS90 3.2 37.8 1.0 HB2 A:CYS90 3.2 37.5 1.0 CB A:CYS93 3.3 42.3 1.0 H A:CYS27 3.3 42.9 1.0 HB2 A:CYS24 3.3 36.6 1.0 CB A:CYS27 3.3 44.1 1.0 HB3 A:GLN92 3.6 39.7 1.0 HB3 A:GLN29 3.7 41.8 1.0 HB3 A:SER95 3.8 49.2 1.0 N A:CYS27 3.8 43.8 1.0 N A:CYS93 3.8 41.7 1.0 H A:GLN29 4.1 42.7 1.0 HB2 A:CYS93 4.1 43.5 1.0 HB2 A:GLN29 4.1 43.0 1.0 CA A:CYS93 4.1 43.1 1.0 HB2 A:CYS27 4.1 45.0 1.0 CA A:CYS27 4.1 43.3 1.0 H A:SER95 4.2 46.3 1.0 CB A:GLN26 4.3 45.6 1.0 H A:GLY28 4.3 42.7 1.0 H A:GLN26 4.3 42.4 1.0 CB A:GLN29 4.4 42.2 1.0 H A:GLY94 4.4 42.7 1.0 HD11 A:LEU97 4.5 43.1 1.0 H A:GLN92 4.6 38.9 1.0 CA A:CYS24 4.6 36.5 1.0 CB A:GLN92 4.6 40.5 1.0 HE21 A:GLN92 4.6 42.0 1.0 CA A:CYS90 4.7 37.9 1.0 CB A:SER95 4.7 49.8 1.0 C A:GLN26 4.7 45.0 1.0 HB2 A:SER95 4.7 50.9 1.0 HB2 A:GLN26 4.8 46.4 1.0 C A:CYS93 4.8 43.8 1.0 N A:GLY28 4.8 43.7 1.0 C A:CYS27 4.8 43.7 1.0 CA A:GLN26 4.8 44.8 1.0 N A:GLN26 4.9 43.1 1.0 N A:GLY94 4.9 43.5 1.0 N A:GLN29 4.9 42.9 1.0 C A:GLN92 4.9 42.0 1.0 HD23 A:LEU97 4.9 42.3 1.0 HA A:CYS93 4.9 44.2 1.0 C A:CYS24 5.0 37.9 1.0 HA A:CYS27 5.0 44.6 1.0 HA A:CYS90 5.0 37.5 1.0

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


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:51.9 occ:1.00 SG B:CYS27 2.2 56.0 1.0 SG B:CYS90 2.3 50.7 1.0 SG B:CYS93 2.3 50.4 1.0 SG B:CYS24 2.4 54.8 1.0 H B:CYS93 3.0 51.4 1.0 HB3 B:CYS24 3.0 55.1 1.0 HB3 B:CYS93 3.1 53.5 1.0 HB3 B:CYS90 3.2 50.5 1.0 HB3 B:CYS27 3.2 57.0 1.0 CB B:CYS24 3.2 54.2 1.0 CB B:CYS90 3.2 49.7 1.0 CB B:CYS93 3.3 52.8 1.0 HB2 B:CYS90 3.3 48.5 1.0 CB B:CYS27 3.3 56.5 1.0 HB2 B:CYS24 3.3 53.1 1.0 H B:CYS27 3.4 53.9 1.0 HB3 B:GLN92 3.4 57.0 1.0 HB3 B:GLN29 3.6 57.7 1.0 N B:CYS93 3.6 52.8 1.0 N B:CYS27 3.9 55.8 1.0 HB2 B:GLN29 3.9 60.0 1.0 HB3 B:SER95 4.0 50.1 1.0 H B:GLN29 4.0 54.6 1.0 CA B:CYS93 4.0 53.8 1.0 HB2 B:CYS27 4.0 58.4 1.0 HB2 B:CYS93 4.1 54.6 1.0 CA B:CYS27 4.1 56.1 1.0 H B:SER95 4.2 50.5 1.0 H B:GLY28 4.2 51.9 1.0 CB B:GLN29 4.3 58.9 1.0 HE21 B:GLN92 4.3 65.4 1.0 H B:GLY94 4.3 50.1 1.0 H B:GLN92 4.4 51.4 1.0 CB B:GLN92 4.4 58.2 1.0 CB B:GLN26 4.5 56.4 1.0 H B:GLN26 4.5 53.9 1.0 HD11 B:LEU97 4.6 43.2 1.0 CA B:CYS24 4.6 52.9 1.0 CA B:CYS90 4.6 48.2 1.0 C B:GLN92 4.7 55.7 1.0 C B:CYS93 4.7 53.3 1.0 N B:GLY28 4.8 53.1 1.0 C B:CYS27 4.8 54.8 1.0 HB2 B:SER95 4.8 52.4 1.0 C B:GLN26 4.8 57.2 1.0 N B:GLN29 4.8 54.3 1.0 N B:GLY94 4.8 51.1 1.0 CB B:SER95 4.8 50.5 1.0 HA B:CYS93 4.8 55.9 1.0 HB2 B:GLN92 4.9 57.2 1.0 HG2 B:GLN92 4.9 63.7 1.0 HG2 B:GLN29 4.9 60.3 1.0 CA B:GLN92 4.9 55.9 1.0 HB2 B:GLN26 4.9 58.1 1.0 HA B:CYS27 5.0 58.2 1.0 HA B:CYS90 5.0 47.2 1.0 N B:GLN92 5.0 52.8 1.0

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


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:60.1 occ:1.00 SG C:CYS93 2.1 60.7 1.0 SG C:CYS27 2.3 62.7 1.0 SG C:CYS90 2.3 60.7 1.0 SG C:CYS24 2.4 62.8 1.0 H C:CYS93 3.0 59.8 1.0 HB3 C:CYS90 3.1 61.3 1.0 HB3 C:CYS93 3.1 60.7 1.0 HB3 C:CYS24 3.1 62.1 1.0 CB C:CYS90 3.1 60.9 1.0 HB3 C:CYS27 3.2 65.4 1.0 HB2 C:CYS90 3.2 61.4 1.0 CB C:CYS93 3.2 61.0 1.0 CB C:CYS24 3.3 62.5 1.0 HB2 C:GLN26 3.3 71.5 1.0 CB C:CYS27 3.3 65.3 1.0 H C:CYS27 3.4 68.0 1.0 HB2 C:CYS24 3.4 61.9 1.0 HB3 C:GLN92 3.6 57.0 1.0 HB3 C:SER95 3.7 68.5 1.0 N C:CYS93 3.7 60.2 1.0 HB3 C:GLN29 3.7 59.1 1.0 N C:CYS27 3.9 68.3 1.0 CA C:CYS93 4.0 61.1 1.0 HB2 C:CYS93 4.0 61.9 1.0 H C:SER95 4.0 66.8 1.0 HB2 C:GLN29 4.1 58.7 1.0 H C:GLN29 4.1 60.6 1.0 HB2 C:CYS27 4.1 64.9 1.0 CA C:CYS27 4.2 66.7 1.0 H C:GLY94 4.3 63.0 1.0 H C:GLY28 4.3 64.1 1.0 CB C:GLN26 4.3 73.1 1.0 CB C:GLN29 4.4 58.9 1.0 H C:GLN26 4.4 71.7 1.0 HE21 C:GLN92 4.4 55.1 1.0 H C:GLN92 4.5 57.2 1.0 CB C:GLN92 4.5 57.0 1.0 CB C:SER95 4.6 69.8 1.0 HB2 C:SER95 4.6 69.9 1.0 CA C:CYS90 4.6 60.4 1.0 C C:CYS93 4.7 62.7 1.0 HB3 C:GLN26 4.7 73.2 1.0 CA C:CYS24 4.7 64.2 1.0 N C:GLY94 4.7 63.9 1.0 C C:GLN26 4.7 71.6 1.0 C C:GLN92 4.8 58.8 1.0 N C:GLY28 4.8 63.6 1.0 HA C:CYS93 4.8 61.3 1.0 C C:CYS27 4.8 65.0 1.0 N C:SER95 4.9 67.6 1.0 CA C:GLN26 4.9 72.8 1.0 N C:GLN29 4.9 60.6 1.0 HA C:CYS90 5.0 60.1 1.0 N C:GLN26 5.0 72.6 1.0 HA C:CYS27 5.0 67.4 1.0 HG2 C:GLN92 5.0 56.5 1.0 HB2 C:GLN92 5.0 56.6 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