Chlorine 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:

Zinc

(Zn)

3 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11A, PDB code: 8ou4:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl202 b:99.4 occ:1.00 CL1 A:W2F202 0.0 99.4 1.0 C8 A:W2F202 1.7 87.5 1.0 H7 A:W2F202 1.9 66.0 1.0 N2 A:W2F202 2.6 64.6 1.0 C9 A:W2F202 2.7 91.4 1.0 C7 A:W2F202 2.7 79.0 1.0 H8 A:W2F202 2.8 92.3 1.0 HD2 A:PHE77 3.1 65.4 1.0 C6 A:W2F202 3.1 69.0 1.0 HZ2 A:TRP85 3.3 51.9 1.0 HG2 A:PRO51 3.5 62.3 0.5 HG2 A:PRO51 3.5 62.3 0.5 HD2 A:PRO51 3.7 59.1 0.5 HD2 A:PRO51 3.7 59.1 0.5 HB2 A:PHE77 3.7 59.8 1.0 CZ2 A:TRP85 3.9 50.1 1.0 H5 A:W2F202 3.9 58.2 1.0 C1 A:W2F202 3.9 59.6 1.0 CD2 A:PHE77 3.9 66.7 1.0 C10 A:W2F202 4.0 91.5 1.0 HH2 A:TRP85 4.0 51.8 1.0 C12 A:W2F202 4.0 82.5 1.0 HD3 A:PRO51 4.2 58.5 0.5 HD3 A:PRO51 4.2 58.5 0.5 CD A:PRO51 4.2 60.0 0.5 CD A:PRO51 4.2 60.0 0.5 CH2 A:TRP85 4.2 50.5 1.0 O3 A:W2F202 4.3 60.3 1.0 CG A:PRO51 4.3 62.6 0.5 CG A:PRO51 4.3 62.6 0.5 C5 A:W2F202 4.3 57.3 1.0 C2 A:W2F202 4.3 59.3 1.0 O1 A:W2F202 4.3 65.3 1.0 H6 A:W2F202 4.5 56.7 1.0 C11 A:W2F202 4.5 86.9 1.0 CB A:PHE77 4.5 61.0 1.0 H1 A:W2F202 4.6 58.9 1.0 O A:GLU76 4.7 58.1 1.0 HE2 A:PHE77 4.7 71.9 1.0 HB2 A:ASN50 4.7 57.5 1.0 HB3 A:PHE77 4.7 60.6 1.0 CG A:PHE77 4.7 65.3 1.0 HG3 A:PRO51 4.7 63.0 0.5 HG3 A:PRO51 4.7 63.0 0.5 H10 A:W2F202 4.8 80.7 1.0 CE2 A:PHE77 4.8 71.3 1.0 CE2 A:TRP85 4.8 48.4 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl202 b:83.2 occ:1.00 CL1 B:W2F202 0.0 83.2 1.0 C8 B:W2F202 1.7 72.1 1.0 H7 B:W2F202 1.8 54.0 1.0 N2 B:W2F202 2.6 52.1 1.0 C9 B:W2F202 2.7 75.0 1.0 C7 B:W2F202 2.7 65.0 1.0 H8 B:W2F202 2.8 75.9 1.0 C6 B:W2F202 3.1 57.3 1.0 HG2 B:PRO51 3.3 47.0 1.0 HD2 B:PRO51 3.3 44.8 1.0 HZ2 B:TRP85 3.4 53.5 1.0 HB2 B:PHE77 3.7 52.8 1.0 C1 B:W2F202 3.8 48.7 1.0 CD B:PRO51 3.9 45.4 1.0 HD3 B:PRO51 3.9 43.7 1.0 CZ2 B:TRP85 3.9 52.2 1.0 O3 B:W2F202 3.9 50.5 1.0 C10 B:W2F202 4.0 75.2 1.0 C12 B:W2F202 4.0 68.5 1.0 CG B:PRO51 4.0 46.4 1.0 H5 B:W2F202 4.0 47.2 1.0 HH2 B:TRP85 4.1 54.2 1.0 C2 B:W2F202 4.2 48.0 1.0 HB2 B:ASN50 4.3 43.2 1.0 O1 B:W2F202 4.3 57.8 1.0 CH2 B:TRP85 4.3 53.1 1.0 C5 B:W2F202 4.4 46.0 1.0 CB B:PHE77 4.5 53.4 1.0 C11 B:W2F202 4.5 72.4 1.0 HG3 B:PRO51 4.5 46.5 1.0 HB3 B:PHE77 4.6 52.5 1.0 H1 B:W2F202 4.6 47.9 1.0 H6 B:W2F202 4.7 46.3 1.0 H10 B:W2F202 4.8 67.3 1.0 O B:GLU76 4.8 52.5 1.0 CG B:PHE77 4.8 56.2 1.0 CE2 B:TRP85 4.9 51.0 1.0 HB2 B:PRO51 5.0 49.1 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