Chlorine in PDB 5hxb: Cereblon in Complex with DDB1, Cc-885, and GSPT1

The structure of Cereblon in Complex with DDB1, Cc-885, and GSPT1, PDB code: 5hxb was solved by P.P.Chamberlain, M.Matyskiela, B.Pagarigan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.60
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.747, 111.522, 175.057, 90.00, 95.81, 90.00
R / Rfree (%)	22.4 / 27.3

The structure of Cereblon in Complex with DDB1, Cc-885, and GSPT1 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Chlorine atom in the Cereblon in Complex with DDB1, Cc-885, and GSPT1 (pdb code 5hxb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Cereblon in Complex with DDB1, Cc-885, and GSPT1, PDB code: 5hxb:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Cereblon in Complex with DDB1, Cc-885, and GSPT1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cereblon in Complex with DDB1, Cc-885, and GSPT1 within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cl502 b:0.5 occ:1.00 CL1 Z:85C502 0.0 0.5 1.0 C18 Z:85C502 1.7 0.4 1.0 CG X:LYS628 2.5 1.0 1.0 C19 Z:85C502 2.7 0.9 1.0 C17 Z:85C502 2.7 0.2 1.0 N X:LYS628 2.9 0.8 1.0 CD X:LYS628 2.9 0.3 1.0 C22 Z:85C502 3.0 0.9 1.0 CB X:LYS628 3.3 96.6 1.0 C X:GLY627 3.5 0.4 1.0 CA X:LYS628 3.6 93.0 1.0 O X:GLN534 3.7 87.9 1.0 CA X:GLY627 3.8 0.6 1.0 C20 Z:85C502 4.0 0.8 1.0 C16 Z:85C502 4.0 0.9 1.0 CE X:LYS628 4.0 0.2 1.0 N X:GLY627 4.1 0.1 1.0 O X:ILE626 4.2 0.1 1.0 O X:GLY627 4.3 0.5 1.0 C X:ILE626 4.5 97.2 1.0 C21 Z:85C502 4.5 0.6 1.0 CE2 X:PHE606 4.6 91.0 1.0 CD2 X:PHE606 4.6 91.0 1.0 C X:GLN534 4.8 86.1 1.0 C X:LYS628 4.8 89.1 1.0

Chlorine binding site 2 out of 2 in the Cereblon in Complex with DDB1, Cc-885, and GSPT1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cereblon in Complex with DDB1, Cc-885, and GSPT1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl502 b:0.4 occ:1.00 CL1 C:85C502 0.0 0.4 1.0 C18 C:85C502 1.7 0.2 1.0 C17 C:85C502 2.7 0.9 1.0 C19 C:85C502 2.7 0.4 1.0 C22 C:85C502 3.0 0.8 1.0 C16 C:85C502 4.0 0.6 1.0 C20 C:85C502 4.0 0.7 1.0 O C:PRO352 4.1 96.3 1.0 CB C:PRO352 4.4 83.5 1.0 C21 C:85C502 4.5 0.8 1.0 CE1 C:HIS353 4.5 1.0 1.0 C C:PRO352 4.6 84.0 1.0 NE2 C:HIS353 4.6 0.1 1.0 CG1 A:VAL536 4.7 60.5 1.0 O4 C:85C502 4.9 78.0 1.0 ND1 C:HIS353 5.0 1.0 1.0 CA C:PRO352 5.0 82.4 1.0 CE2 C:PHE102 5.0 99.6 1.0

M.E.Matyskiela, G.Lu, T.Ito, B.Pagarigan, C.C.Lu, K.Miller, W.Fang, N.Y.Wang, D.Nguyen, J.Houston, G.Carmel, T.Tran, M.Riley, L.Nosaka, G.C.Lander, S.Gaidarova, S.Xu, A.L.Ruchelman, H.Handa, J.Carmichael, T.O.Daniel, B.E.Cathers, A.Lopez-Girona, P.P.Chamberlain. A Novel Cereblon Modulator Recruits GSPT1 to the CRL4(Crbn) Ubiquitin Ligase. Nature V. 535 252 2016.
ISSN: ESSN 1476-4687
PubMed: 27338790
DOI: 10.1038/NATURE18611