Chlorine in PDB 8rdq: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B, PDB code: 8rdq was solved by L.Bischof, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.61 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.536, 59.8, 88.01, 90, 90, 90
R / Rfree (%)	20.5 / 24.9

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Chlorine atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B (pdb code 8rdq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B, PDB code: 8rdq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B


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 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:81.2 occ:1.00 CL2 A:YQO202 0.0 81.2 1.0 C12 A:YQO202 1.7 76.7 1.0 C11 A:YQO202 2.7 81.8 1.0 C7 A:YQO202 2.8 70.6 1.0 N2 A:YQO202 2.9 57.9 1.0 C6 A:YQO202 3.2 61.1 1.0 C10 A:YQO202 4.0 83.3 1.0 C8 A:YQO202 4.0 75.3 1.0 O2 A:YQO202 4.2 54.0 1.0 CD A:PRO51 4.2 46.6 1.0 ND2 A:ASN50 4.3 40.9 1.0 C9 A:YQO202 4.5 79.8 1.0 CG A:ASN50 4.6 42.8 1.0 C5 A:YQO202 4.7 56.2 1.0 CG A:PRO51 4.7 49.2 1.0 CB A:ASN50 4.8 42.2 1.0 CB A:ALA52 4.9 50.4 1.0 N A:ALA52 5.0 51.1 1.0

Chlorine binding site 2 out of 4 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B


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 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:93.3 occ:1.00 CL1 A:YQO202 0.0 93.3 1.0 C10 A:YQO202 1.7 83.3 1.0 C9 A:YQO202 2.7 79.8 1.0 C11 A:YQO202 2.7 81.8 1.0 C8 A:YQO202 4.0 75.3 1.0 C12 A:YQO202 4.0 76.7 1.0 C7 A:YQO202 4.5 70.6 1.0 CE2 A:PHE77 4.9 53.8 1.0

Chlorine binding site 3 out of 4 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:72.4 occ:1.00 CL2 B:YQO202 0.0 72.4 1.0 C12 B:YQO202 1.7 63.8 1.0 C11 B:YQO202 2.7 69.0 1.0 N2 B:YQO202 2.7 46.8 1.0 C7 B:YQO202 2.8 59.1 1.0 C6 B:YQO202 3.1 50.1 1.0 ND2 B:ASN50 3.9 33.7 1.0 CD B:PRO51 3.9 32.3 1.0 C10 B:YQO202 4.0 70.8 1.0 C8 B:YQO202 4.0 62.9 1.0 O2 B:YQO202 4.0 44.1 1.0 CG B:ASN50 4.2 33.0 1.0 CB B:ASN50 4.5 31.7 1.0 CG B:PRO51 4.5 34.0 1.0 C9 B:YQO202 4.5 67.3 1.0 N B:ALA52 4.6 33.0 1.0 C5 B:YQO202 4.6 46.7 1.0 N B:PRO51 4.6 32.4 1.0 CB B:ALA52 4.7 34.3 1.0 CB B:PRO51 4.8 35.3 1.0 OD1 B:ASN50 4.8 33.8 1.0

Chlorine binding site 4 out of 4 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Spiro-Isoxazol Based Compound 8B within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:76.2 occ:1.00 CL1 B:YQO202 0.0 76.2 1.0 C10 B:YQO202 1.7 70.8 1.0 C9 B:YQO202 2.7 67.3 1.0 C11 B:YQO202 2.7 69.0 1.0 C8 B:YQO202 4.0 62.9 1.0 C12 B:YQO202 4.0 63.8 1.0 CE2 B:PHE77 4.3 49.2 1.0 C7 B:YQO202 4.5 59.1 1.0 CD2 B:PHE77 4.9 46.7 1.0

R.Shevalev, L.Bischof, A.Sapegin, A.Bunev, G.Olga, G.Kantin, S.Kalinin, M.D.Hartmann. Discovery and Characterization of Potent Spiro-Isoxazole-Based Cereblon Ligands with A Novel Binding Mode. Eur.J.Med.Chem. V. 270 16328 2024.
ISSN: ISSN 0223-5234
PubMed: 38552426
DOI: 10.1016/J.EJMECH.2024.116328