Fluorine in PDB 8rqc: Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2

The structure of Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2, PDB code: 8rqc was solved by H.Furihata, A.Kroupova, D.Zollman, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.44 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.585, 142.842, 56.693, 90, 112.34, 90
R / Rfree (%)	26.1 / 28.6

The structure of Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2 also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Fluorine atom in the Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2 (pdb code 8rqc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2, PDB code: 8rqc:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:81.3 occ:1.00 F A:QFC602 0.0 81.3 1.0 C A:QFC602 1.3 74.1 1.0 C5 A:QFC602 2.4 73.0 1.0 C1 A:QFC602 2.4 79.2 1.0 C30 A:QFC602 2.6 71.4 1.0 N A:QFC602 2.8 71.9 1.0 C4 A:QFC602 3.7 72.9 1.0 C2 A:QFC602 3.7 78.8 1.0 CB A:ASP149 3.9 102.4 1.0 C29 A:QFC602 3.9 72.1 1.0 C3 A:QFC602 4.2 82.0 1.0 CD1 A:ILE154 4.2 82.2 1.0 C6 A:QFC602 4.3 63.7 1.0 O A:ASP149 4.4 106.3 1.0 CE2 A:PHE102 4.5 69.7 1.0 CG1 A:ILE154 4.6 75.6 1.0 C A:ASP149 4.8 110.0 1.0 OD2 A:ASP149 4.8 97.9 1.0 CD2 A:PHE102 4.8 67.3 1.0 CA A:ASP149 4.9 104.8 1.0 CG A:ASP149 4.9 102.4 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2 within 5.0Å range: probe atom residue distance (Å) B Occ D:F602 b:63.0 occ:1.00 F D:QFC602 0.0 63.0 1.0 C D:QFC602 1.3 62.5 1.0 C5 D:QFC602 2.4 60.0 1.0 C1 D:QFC602 2.4 62.0 1.0 C6 D:QFC602 2.5 61.3 1.0 N D:QFC602 2.8 62.6 1.0 C30 D:QFC602 3.7 58.0 1.0 C4 D:QFC602 3.7 60.1 1.0 C2 D:QFC602 3.7 61.9 1.0 CE1 D:PHE102 3.8 59.7 1.0 CD1 D:ILE154 4.0 53.7 1.0 O D:ASP149 4.0 55.7 1.0 C7 D:QFC602 4.1 64.2 1.0 CD2 D:PHE150 4.2 62.1 1.0 C3 D:QFC602 4.2 57.2 1.0 CD1 D:PHE102 4.4 57.1 1.0 CB D:PHE150 4.6 56.7 1.0 CZ D:PHE102 4.6 55.8 1.0 C D:ASP149 4.7 58.5 1.0 CG1 D:ILE154 4.7 55.0 1.0 CB D:ILE152 4.7 57.8 1.0 CG D:PHE150 4.7 61.2 1.0 CD1 D:ILE152 4.7 63.8 1.0 CB D:ASP149 4.9 56.6 1.0 C29 D:QFC602 4.9 54.8 1.0

A.Kroupova, V.Spiteri, H.Furihata, D.Darren, S.Ramachandran, Z.Rutter, S.Chakraborti, K.Haubrich, J.Pethe, D.Gonzales, A.Wijaya, M.Rodriguez-Rios, D.Lynch, W.Farnaby, M.Nakasone, D.Zollman, A.Ciulli. Design of A Cereblon Construct For Crystallographic and Biophysical Studies of Protein Degraders To Be Published.