Fluorine in PDB 8oua: Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F, PDB code: 8oua 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)	49.30 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.422, 59.472, 88.147, 90, 90, 90
R / Rfree (%)	18.4 / 23.8

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

Zinc

(Zn)

3 atoms

The binding sites of Fluorine atom in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F (pdb code 8oua). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F, PDB code: 8oua:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:67.4 occ:1.00 F1 A:W0Z202 0.0 67.4 1.0 C12 A:W0Z202 1.3 59.9 1.0 H7 A:W0Z202 1.8 35.9 1.0 C11 A:W0Z202 2.4 82.0 1.0 C7 A:W0Z202 2.4 53.0 1.0 H11 A:W0Z202 2.4 80.3 1.0 N2 A:W0Z202 2.5 35.9 1.0 C6 A:W0Z202 2.9 42.4 1.0 O2 A:W0Z202 2.9 85.8 1.0 HD2 A:PHE77 2.9 46.0 1.0 C13 A:W0Z202 3.0 78.3 1.0 H13 A:W0Z202 3.3 80.5 1.0 HB2 A:PHE77 3.4 36.5 1.0 HZ2 A:TRP85 3.4 36.9 1.0 HG2 A:PRO51 3.4 47.8 1.0 HD2 A:PRO51 3.6 45.7 1.0 CD2 A:PHE77 3.6 44.6 1.0 C8 A:W0Z202 3.6 60.3 1.0 C10 A:W0Z202 3.6 83.3 1.0 C2 A:W0Z202 3.7 29.4 1.0 H12 A:W0Z202 3.8 80.5 1.0 O3 A:W0Z202 3.9 40.2 1.0 H2 A:W0Z202 3.9 32.7 1.0 HD3 A:PRO51 3.9 45.6 1.0 CZ2 A:TRP85 4.0 35.2 1.0 CD A:PRO51 4.0 48.1 1.0 C3 A:W0Z202 4.0 37.3 1.0 O1 A:W0Z202 4.1 40.6 1.0 C9 A:W0Z202 4.1 62.7 1.0 CB A:PHE77 4.1 34.0 1.0 CG A:PRO51 4.1 49.7 1.0 CG A:PHE77 4.2 42.7 1.0 HH2 A:TRP85 4.2 39.9 1.0 HB3 A:PHE77 4.3 36.4 1.0 C1 A:W0Z202 4.3 33.7 1.0 H8 A:W0Z202 4.4 59.1 1.0 CH2 A:TRP85 4.4 41.3 1.0 CE2 A:PHE77 4.4 53.4 1.0 H3 A:W0Z202 4.4 32.8 1.0 HE2 A:PHE77 4.4 51.7 1.0 HB2 A:ASN50 4.5 38.0 1.0 HG3 A:PRO51 4.5 47.9 1.0 O A:GLU76 4.6 42.0 1.0 H1 A:W0Z202 4.6 32.6 1.0 N3 A:W0Z202 4.8 97.6 1.0 CE2 A:TRP85 4.8 36.9 1.0 H9 A:W0Z202 4.9 91.9 1.0 HE1 A:TRP85 5.0 34.5 1.0

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


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:74.9 occ:1.00 F2 A:W0Z202 0.0 74.9 1.0 C9 A:W0Z202 1.3 62.7 1.0 C8 A:W0Z202 2.3 60.3 1.0 C10 A:W0Z202 2.4 83.3 1.0 H10 A:W0Z202 2.5 92.4 1.0 H8 A:W0Z202 2.5 59.1 1.0 N3 A:W0Z202 2.8 97.6 1.0 HB2 A:ALA52 3.1 38.0 1.0 C7 A:W0Z202 3.6 53.0 1.0 C11 A:W0Z202 3.7 82.0 1.0 H9 A:W0Z202 3.7 91.9 1.0 HB3 A:ALA52 3.7 38.0 1.0 CB A:ALA52 3.9 39.3 1.0 C12 A:W0Z202 4.1 59.9 1.0 H A:ALA52 4.3 40.3 1.0 HD22 A:ASN50 4.4 35.7 1.0 HB1 A:ALA52 4.4 37.9 1.0 ND2 A:ASN50 4.6 33.3 1.0 HD2 A:PRO51 4.6 45.7 1.0 HD21 A:ASN50 4.7 35.7 1.0 N A:ALA52 4.7 43.0 1.0 O2 A:W0Z202 4.7 85.8 1.0 C6 A:W0Z202 4.8 42.4 1.0 CA A:ALA52 4.9 35.1 1.0 O1 A:W0Z202 5.0 40.6 1.0

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


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:65.0 occ:1.00 F1 B:W0Z202 0.0 65.0 1.0 C12 B:W0Z202 1.4 47.1 1.0 H7 B:W0Z202 1.8 34.6 1.0 H11 B:W0Z202 2.4 77.3 1.0 C11 B:W0Z202 2.4 75.0 1.0 C7 B:W0Z202 2.4 41.0 1.0 N2 B:W0Z202 2.5 34.2 1.0 O2 B:W0Z202 2.8 87.9 1.0 C6 B:W0Z202 2.9 39.5 1.0 C13 B:W0Z202 2.9 73.3 1.0 HZ2 B:TRP85 3.2 34.4 1.0 HD2 B:PHE77 3.3 51.7 1.0 H13 B:W0Z202 3.3 77.5 1.0 HD2 B:PRO51 3.4 35.8 1.0 HG2 B:PRO51 3.6 35.9 1.0 C10 B:W0Z202 3.7 69.1 1.0 C8 B:W0Z202 3.7 59.8 1.0 HB2 B:PHE77 3.7 42.0 1.0 CZ2 B:TRP85 3.8 33.9 1.0 H12 B:W0Z202 3.8 77.5 1.0 C2 B:W0Z202 3.8 30.6 1.0 HH2 B:TRP85 3.8 39.4 1.0 H2 B:W0Z202 3.9 32.1 1.0 HD3 B:PRO51 4.0 35.7 1.0 CD2 B:PHE77 4.0 51.4 1.0 CD B:PRO51 4.0 37.1 1.0 CH2 B:TRP85 4.1 39.8 1.0 O3 B:W0Z202 4.1 31.4 1.0 C9 B:W0Z202 4.1 71.9 1.0 O1 B:W0Z202 4.2 41.1 1.0 C3 B:W0Z202 4.2 32.0 1.0 CG B:PRO51 4.3 38.4 1.0 C1 B:W0Z202 4.3 35.6 1.0 HB2 B:ASN50 4.4 24.6 1.0 H1 B:W0Z202 4.4 32.1 1.0 H8 B:W0Z202 4.4 56.6 1.0 CB B:PHE77 4.5 41.9 1.0 H3 B:W0Z202 4.5 32.5 1.0 CG B:PHE77 4.6 46.6 1.0 HB3 B:PHE77 4.6 41.9 1.0 CE2 B:TRP85 4.7 30.9 1.0 HE2 B:PHE77 4.8 55.3 1.0 N3 B:W0Z202 4.8 94.8 1.0 CE2 B:PHE77 4.8 58.7 1.0 HG3 B:PRO51 4.8 35.9 1.0 O B:GLU76 4.8 37.2 1.0 H9 B:W0Z202 4.9 85.4 1.0

Fluorine binding site 4 out of 4 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11F within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:61.0 occ:1.00 F2 B:W0Z202 0.0 61.0 1.0 C9 B:W0Z202 1.4 71.9 1.0 H10 B:W0Z202 2.3 85.7 1.0 C10 B:W0Z202 2.3 69.1 1.0 C8 B:W0Z202 2.4 59.8 1.0 H8 B:W0Z202 2.6 56.6 1.0 N3 B:W0Z202 2.6 94.8 1.0 HB2 B:ALA52 3.3 28.0 1.0 H9 B:W0Z202 3.5 85.4 1.0 HB3 B:ALA52 3.6 28.1 1.0 C11 B:W0Z202 3.6 75.0 1.0 C7 B:W0Z202 3.6 41.0 1.0 HE3 B:MET54 3.8 72.7 1.0 HD22 B:ASN50 3.9 32.9 1.0 CB B:ALA52 3.9 28.1 1.0 HE2 B:MET54 4.0 71.7 1.0 C12 B:W0Z202 4.1 47.1 1.0 CE B:MET54 4.3 75.9 1.0 HB1 B:ALA52 4.3 28.1 1.0 ND2 B:ASN50 4.3 33.6 1.0 H B:ALA52 4.6 26.8 1.0 HD21 B:ASN50 4.6 33.0 1.0 O2 B:W0Z202 4.7 87.9 1.0 C6 B:W0Z202 4.8 39.5 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