Zinc in PDB 7u8f: Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2) and the Molecular Glue DKY709

The structure of Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2) and the Molecular Glue DKY709, PDB code: 7u8f was solved by X.Ma, E.Ornelas, M.C.Clifton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.89 / 3.15
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	180.892, 180.892, 555.884, 90, 90, 120
R / Rfree (%)	21.3 / 24.3

The binding sites of Zinc atom in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2) and the Molecular Glue DKY709 (pdb code 7u8f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2) and the Molecular Glue DKY709, PDB code: 7u8f:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2) and the Molecular Glue DKY709


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2) and the Molecular Glue DKY709 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:115.4 occ:1.00 SG A:CYS326 2.3 91.5 1.0 SG A:CYS391 2.3 100.0 1.0 SG A:CYS394 2.3 104.1 1.0 SG A:CYS323 2.3 130.3 1.0 CB A:CYS323 2.9 107.7 1.0 CB A:CYS391 3.1 96.9 1.0 CB A:CYS326 3.2 95.4 1.0 N A:CYS326 3.6 105.2 1.0 CB A:CYS394 3.8 90.5 1.0 CA A:CYS326 4.0 104.2 1.0 N A:CYS394 4.1 91.1 1.0 CA A:CYS323 4.4 98.9 1.0 CA A:CYS394 4.5 90.9 1.0 CA A:CYS391 4.6 90.1 1.0 N A:GLN327 4.7 109.4 1.0 C A:GLN325 4.7 93.6 1.0 CB A:GLN325 4.7 96.3 1.0 C A:CYS326 4.8 108.6 1.0 CB A:ILE393 4.8 100.3 1.0 C A:CYS323 4.9 96.2 1.0 CG2 A:ILE393 5.0 113.9 1.0

Zinc binding site 2 out of 4 in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2) and the Molecular Glue DKY709


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2) and the Molecular Glue DKY709 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:92.6 occ:1.00 NE2 C:HIS162 2.0 87.5 1.0 NE2 C:HIS158 2.1 114.1 1.0 SG C:CYS142 2.3 80.6 1.0 SG C:CYS145 2.3 78.6 1.0 CD2 C:HIS158 2.7 102.6 1.0 CD2 C:HIS162 2.8 98.3 1.0 CB C:CYS142 3.1 108.1 1.0 CE1 C:HIS162 3.1 103.5 1.0 CE1 C:HIS158 3.2 122.4 1.0 CB C:CYS145 3.3 91.7 1.0 N C:CYS145 3.4 110.9 1.0 CG C:HIS158 3.9 89.0 1.0 CA C:CYS145 3.9 99.0 1.0 CG C:HIS162 4.0 103.5 1.0 ND1 C:HIS162 4.1 116.1 1.0 ND1 C:HIS158 4.1 112.2 1.0 CB C:GLN144 4.3 92.5 1.0 N C:GLY146 4.5 98.4 1.0 CA C:CYS142 4.5 107.3 1.0 C C:GLN144 4.5 97.9 1.0 CB C:ALA147 4.6 98.5 1.0 C C:CYS145 4.6 94.9 1.0 N C:ALA147 4.7 101.5 1.0 N C:GLN144 4.8 89.1 1.0 CA C:GLN144 4.8 82.8 1.0 C C:CYS142 4.9 98.2 1.0 O C:CYS142 5.0 103.0 1.0

Zinc binding site 3 out of 4 in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2) and the Molecular Glue DKY709


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2) and the Molecular Glue DKY709 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:105.5 occ:1.00 SG D:CYS326 2.3 85.0 1.0 SG D:CYS391 2.3 117.6 1.0 SG D:CYS323 2.3 95.8 1.0 SG D:CYS394 2.3 84.3 1.0 CB D:CYS323 2.9 100.0 1.0 CB D:CYS391 3.0 84.6 1.0 CB D:CYS326 3.3 103.3 1.0 N D:CYS326 3.6 91.4 1.0 CB D:CYS394 3.8 101.7 1.0 N D:CYS394 3.9 85.7 1.0 CA D:CYS326 4.0 96.4 1.0 CA D:CYS323 4.4 96.7 1.0 CA D:CYS394 4.4 95.0 1.0 CA D:CYS391 4.5 84.8 1.0 N D:GLN327 4.7 90.5 1.0 C D:GLN325 4.8 90.5 1.0 CB D:GLN325 4.8 99.9 1.0 CB D:ILE393 4.8 90.3 1.0 C D:CYS326 4.9 93.2 1.0 CB D:THR329 4.9 118.0 1.0 C D:CYS323 4.9 99.5 1.0 OG1 D:THR329 4.9 128.6 1.0 N D:ILE393 4.9 95.1 1.0 C D:ILE393 4.9 96.6 1.0 CB D:SER396 5.0 92.3 1.0 N D:ALA395 5.0 88.1 1.0

Zinc binding site 4 out of 4 in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2) and the Molecular Glue DKY709


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2) and the Molecular Glue DKY709 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:97.4 occ:1.00 NE2 F:HIS162 1.9 95.2 1.0 NE2 F:HIS158 2.1 106.2 1.0 SG F:CYS142 2.3 112.8 1.0 SG F:CYS145 2.3 86.4 1.0 CD2 F:HIS158 2.5 112.3 1.0 CD2 F:HIS162 2.7 102.4 1.0 CE1 F:HIS162 3.0 103.7 1.0 CB F:CYS142 3.0 109.4 1.0 CE1 F:HIS158 3.3 104.3 1.0 N F:CYS145 3.5 118.0 1.0 CB F:CYS145 3.6 89.4 1.0 CG F:HIS158 3.8 84.9 1.0 CG F:HIS162 3.9 107.4 1.0 ND1 F:HIS162 4.0 99.9 1.0 CA F:CYS145 4.1 91.7 1.0 ND1 F:HIS158 4.1 101.0 1.0 CB F:GLN144 4.3 93.8 1.0 CA F:CYS142 4.5 99.9 1.0 C F:GLN144 4.6 99.5 1.0 C F:CYS145 4.6 88.4 1.0 CB F:ALA147 4.6 106.5 1.0 N F:GLN144 4.6 96.7 1.0 CA F:GLN144 4.7 86.3 1.0 C F:CYS142 4.8 105.4 1.0 N F:ALA147 4.9 117.3 1.0 N F:GLY146 4.9 91.0 1.0 O F:CYS142 5.0 113.4 1.0

S.Bonazzi, E.D'hennezel, R.E.Beckwith, L.Xu, A.Fazal, A.Magracheva, R.Ramesh, A.Cernijenko, B.Antonakos, H.E.C.Bhang, R.G.Caro, J.S.Cobb, E.Ornelas, X.Ma, C.A.Wartchow, M.C.Clifton, R.R.Forseth, B.H.Fortnam, H.Lu, A.Csibi, J.Tullai, S.Carbonneau, N.M.Thomsen, J.Larrow, B.Chie-Leon, D.Hainzl, Y.Gu, D.Lu, M.J.Meyer, D.Alexander, J.Kinyamu-Akunda, C.A.Sabatos-Peyton, N.A.Dales, F.J.Zecri, R.K.Jain, J.Shulok, Y.K.Wang, K.Briner, J.A.Porter, J.A.Tallarico, J.A.Engelman, G.Dranoff, J.E.Bradner, M.Visser, J.M.Solomon. Discovery and Characterization of A Selective IKZF2 Glue Degrader For Cancer Immunotherapy Cell Chem Biol 2023.
ISSN: ESSN 2451-9456
DOI: 10.1016/J.CHEMBIOL.2023.02.005