Fluorine in PDB 8ou3: Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D, PDB code: 8ou3 was solved by C.Heim, L.Bischof, S.Maiwald, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.33 / 1.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.793, 59.519, 88.149, 90, 90, 90
R / Rfree (%)	21.5 / 23.8

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D 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 8D (pdb code 8ou3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D, PDB code: 8ou3:

Fluorine binding site 1 out of 1 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D


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 8D within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:50.3 occ:1.00 F1 B:W1T202 0.0 50.3 1.0 C6 B:W1T202 1.3 41.1 1.0 C1 B:W1T202 2.3 46.8 1.0 C5 B:W1T202 2.4 36.1 1.0 N1 B:W1T202 2.6 28.4 1.0 C7 B:W1T202 2.9 30.4 1.0 C2 B:W1T202 3.6 47.3 1.0 CD B:PRO51 3.6 25.1 1.0 C4 B:W1T202 3.6 41.3 1.0 CG B:PRO51 3.8 25.2 1.0 CD2 B:PHE77 3.8 42.1 1.0 C8 B:W1T202 3.9 23.3 1.0 O2 B:W1T202 4.0 25.0 1.0 C3 B:W1T202 4.1 43.6 1.0 CZ2 B:TRP85 4.2 28.3 1.0 O1 B:W1T202 4.2 28.4 1.0 C12 B:W1T202 4.2 23.6 1.0 CE2 B:PHE77 4.5 44.8 1.0 CH2 B:TRP85 4.5 29.7 1.0 C9 B:W1T202 4.6 24.6 1.0 CG B:PHE77 4.7 37.5 1.0 N3 B:W1T202 4.7 59.3 1.0 CB B:PHE77 4.7 34.4 1.0 CB B:PRO51 4.9 24.5 1.0 N B:PRO51 4.9 23.4 1.0 CB B:ASN50 5.0 21.0 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