Fluorine 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:

Zinc

(Zn)

3 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11B, PDB code: 8ou5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11B


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 11B within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:84.6 occ:1.00 F1 A:W1X202 0.0 84.6 1.0 C13 A:W1X202 1.3 82.3 1.0 F2 A:W1X202 2.1 82.1 1.0 F3 A:W1X202 2.1 78.9 1.0 H8 A:W1X202 2.3 81.7 1.0 C8 A:W1X202 2.4 80.4 1.0 C9 A:W1X202 2.7 81.7 1.0 HE1 A:HIS96 3.6 53.9 1.0 C7 A:W1X202 3.7 73.9 1.0 CE1 A:HIS96 4.1 53.2 1.0 C10 A:W1X202 4.1 82.9 1.0 ND1 A:HIS96 4.2 53.8 1.0 O1 A:W1X202 4.3 67.3 1.0 C6 A:W1X202 4.3 66.3 1.0 HZ2 A:TRP99 4.6 47.5 1.0 HD21 A:ASN50 4.7 53.8 1.0 HN31 A:W1X202 4.7 87.0 1.0 C12 A:W1X202 4.8 76.1 1.0 HE1 A:TRP99 4.8 47.5 1.0 N3 A:W1X202 4.9 87.4 1.0 HD13 A:ILE87 4.9 57.9 1.0 C11 A:W1X202 4.9 79.6 1.0 HZ A:PHE56 5.0 54.5 1.0 HG12 A:ILE87 5.0 53.8 1.0

Fluorine binding site 2 out of 6 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11B


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 11B within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:82.1 occ:1.00 F2 A:W1X202 0.0 82.1 1.0 C13 A:W1X202 1.3 82.3 1.0 F1 A:W1X202 2.1 84.6 1.0 F3 A:W1X202 2.1 78.9 1.0 C8 A:W1X202 2.4 80.4 1.0 O1 A:W1X202 2.7 67.3 1.0 HD21 A:ASN50 2.9 53.8 1.0 HE1 A:HIS96 3.0 53.9 1.0 HZ2 A:TRP99 3.0 47.5 1.0 HZ A:PHE56 3.1 54.5 1.0 C7 A:W1X202 3.1 73.9 1.0 C6 A:W1X202 3.2 66.3 1.0 C9 A:W1X202 3.4 81.7 1.0 H8 A:W1X202 3.5 81.7 1.0 ND2 A:ASN50 3.6 55.3 1.0 HD22 A:ASN50 3.6 56.1 1.0 CE1 A:HIS96 3.8 53.2 1.0 CZ A:PHE56 3.8 53.9 1.0 CZ2 A:TRP99 4.0 46.5 1.0 HE2 A:PHE56 4.0 54.8 1.0 ND1 A:HIS96 4.2 53.8 1.0 CE2 A:PHE56 4.3 53.9 1.0 HE1 A:TRP99 4.4 47.5 1.0 C12 A:W1X202 4.4 76.1 1.0 SD A:MET54 4.5 78.7 1.0 N2 A:W1X202 4.5 62.0 1.0 C10 A:W1X202 4.6 82.9 1.0 HH2 A:TRP99 4.7 46.4 1.0 CG A:ASN50 4.8 56.3 1.0 H1 A:W1X202 4.8 56.4 1.0 CE1 A:PHE56 4.8 53.1 1.0 CE2 A:TRP99 4.8 46.0 1.0 CH2 A:TRP99 4.8 45.6 1.0 HE1 A:PHE56 4.9 53.0 1.0 NE1 A:TRP99 4.9 46.6 1.0 HB3 A:ASN50 4.9 52.6 1.0 NE2 A:HIS96 4.9 52.6 1.0 C11 A:W1X202 5.0 79.6 1.0

Fluorine binding site 3 out of 6 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11B


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 11B within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:78.9 occ:1.00 F3 A:W1X202 0.0 78.9 1.0 C13 A:W1X202 1.3 82.3 1.0 F1 A:W1X202 2.1 84.6 1.0 F2 A:W1X202 2.1 82.1 1.0 C8 A:W1X202 2.4 80.4 1.0 HE1 A:TRP99 2.8 47.5 1.0 O1 A:W1X202 2.9 67.3 1.0 C6 A:W1X202 2.9 66.3 1.0 C7 A:W1X202 2.9 73.9 1.0 HE1 A:HIS96 3.0 53.9 1.0 HZ2 A:TRP99 3.1 47.5 1.0 C9 A:W1X202 3.5 81.7 1.0 NE1 A:TRP99 3.5 46.6 1.0 CE1 A:HIS96 3.7 53.2 1.0 H8 A:W1X202 3.7 81.7 1.0 N2 A:W1X202 3.8 62.0 1.0 HG12 A:ILE87 3.8 53.8 1.0 CZ2 A:TRP99 3.8 46.5 1.0 H3 A:W1X202 4.0 54.6 1.0 CE2 A:TRP99 4.0 46.0 1.0 HD13 A:ILE87 4.2 57.9 1.0 H7 A:W1X202 4.2 63.4 1.0 C12 A:W1X202 4.3 76.1 1.0 H1 A:W1X202 4.3 56.4 1.0 HD21 A:ASN50 4.3 53.8 1.0 NE2 A:HIS96 4.4 52.6 1.0 ND1 A:HIS96 4.5 53.8 1.0 C2 A:W1X202 4.5 57.2 1.0 CG1 A:ILE87 4.6 54.9 1.0 C10 A:W1X202 4.7 82.9 1.0 CD1 A:ILE87 4.7 57.2 1.0 HD11 A:ILE87 4.7 57.2 1.0 C3 A:W1X202 4.7 55.0 1.0 CD1 A:TRP99 4.8 45.6 1.0 H11 A:W1X202 4.9 76.2 1.0 HG13 A:ILE87 4.9 54.4 1.0 C11 A:W1X202 5.0 79.6 1.0

Fluorine binding site 4 out of 6 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11B


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 11B within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:88.2 occ:1.00 F1 B:W1X202 0.0 88.2 1.0 C13 B:W1X202 1.3 91.0 1.0 F2 B:W1X202 2.1 93.3 1.0 F3 B:W1X202 2.1 87.4 1.0 O1 B:W1X202 2.3 67.2 1.0 C8 B:W1X202 2.4 85.8 1.0 C6 B:W1X202 2.7 65.0 1.0 HE1 B:TRP99 2.8 44.0 1.0 C7 B:W1X202 2.9 75.3 1.0 HD13 B:ILE87 3.5 60.4 1.0 C9 B:W1X202 3.6 87.2 1.0 HG12 B:ILE87 3.6 54.9 1.0 NE1 B:TRP99 3.6 43.8 1.0 HZ2 B:TRP99 3.7 42.9 1.0 H3 B:W1X202 3.8 52.5 1.0 N2 B:W1X202 3.8 59.3 1.0 H8 B:W1X202 3.8 87.8 1.0 HE1 B:HIS96 4.0 46.9 1.0 CD1 B:ILE87 4.1 60.9 1.0 HD11 B:ILE87 4.2 60.3 1.0 C12 B:W1X202 4.3 77.0 1.0 CG1 B:ILE87 4.3 55.9 1.0 H7 B:W1X202 4.3 61.2 1.0 CE2 B:TRP99 4.4 41.5 1.0 H1 B:W1X202 4.4 54.3 1.0 HD21 B:ASN50 4.4 46.8 1.0 CZ2 B:TRP99 4.4 42.6 1.0 C2 B:W1X202 4.5 55.0 1.0 HG13 B:ILE87 4.5 55.7 1.0 C3 B:W1X202 4.5 52.1 1.0 CE1 B:HIS96 4.6 47.3 1.0 CD1 B:TRP99 4.7 42.2 1.0 C10 B:W1X202 4.7 87.6 1.0 HD1 B:TRP99 4.8 43.1 1.0 H11 B:W1X202 4.8 76.7 1.0 HZ3 B:TRP85 4.9 53.0 1.0 H2 B:W1X202 4.9 53.6 1.0 HH2 B:TRP85 5.0 55.3 1.0

Fluorine binding site 5 out of 6 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 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:F202 b:93.3 occ:1.00 F2 B:W1X202 0.0 93.3 1.0 C13 B:W1X202 1.3 91.0 1.0 F1 B:W1X202 2.1 88.2 1.0 F3 B:W1X202 2.1 87.4 1.0 C8 B:W1X202 2.4 85.8 1.0 H8 B:W1X202 2.4 87.8 1.0 C9 B:W1X202 2.7 87.2 1.0 C7 B:W1X202 3.6 75.3 1.0 HD13 B:ILE87 3.8 60.4 1.0 O1 B:W1X202 4.1 67.2 1.0 C10 B:W1X202 4.1 87.6 1.0 HD11 B:ILE87 4.2 60.3 1.0 C6 B:W1X202 4.2 65.0 1.0 CD1 B:ILE87 4.4 60.9 1.0 HG12 B:ILE87 4.6 54.9 1.0 HE1 B:TRP99 4.7 44.0 1.0 HE1 B:HIS96 4.7 46.9 1.0 C12 B:W1X202 4.8 77.0 1.0 HN31 B:W1X202 4.8 91.9 1.0 C11 B:W1X202 5.0 81.5 1.0 N3 B:W1X202 5.0 91.7 1.0

Fluorine binding site 6 out of 6 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 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:F202 b:87.4 occ:1.00 F3 B:W1X202 0.0 87.4 1.0 C13 B:W1X202 1.3 91.0 1.0 F2 B:W1X202 2.1 93.3 1.0 F1 B:W1X202 2.1 88.2 1.0 C8 B:W1X202 2.4 85.8 1.0 O1 B:W1X202 2.8 67.2 1.0 HD21 B:ASN50 3.2 46.8 1.0 C7 B:W1X202 3.2 75.3 1.0 C9 B:W1X202 3.3 87.2 1.0 H8 B:W1X202 3.3 87.8 1.0 C6 B:W1X202 3.4 65.0 1.0 HZ2 B:TRP99 3.6 42.9 1.0 HD22 B:ASN50 3.7 48.8 1.0 HE1 B:HIS96 3.7 46.9 1.0 HZ B:PHE56 3.7 47.0 1.0 ND2 B:ASN50 3.7 48.7 1.0 HE1 B:TRP99 4.2 44.0 1.0 HE2 B:PHE56 4.3 46.0 1.0 CE1 B:HIS96 4.4 47.3 1.0 CZ B:PHE56 4.4 46.2 1.0 SD B:MET54 4.5 56.9 0.5 C12 B:W1X202 4.5 77.0 1.0 C10 B:W1X202 4.5 87.6 1.0 CZ2 B:TRP99 4.5 42.6 1.0 CE2 B:PHE56 4.7 45.3 1.0 N2 B:W1X202 4.7 59.3 1.0 NE1 B:TRP99 4.9 43.8 1.0 ND1 B:HIS96 4.9 46.5 1.0 CG B:ASN50 5.0 46.6 1.0 C11 B:W1X202 5.0 81.5 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