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Zinc in PDB 8dey: Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2,3) and the Molecular Glue DKY709

Protein crystallography data

The structure of Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2,3) and the Molecular Glue DKY709, PDB code: 8dey was solved by M.C.Clifton, X.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.15 / 3.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 96.476, 96.227, 155.598, 90, 93.46, 90
R / Rfree (%) 29.9 / 34.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2,3) and the Molecular Glue DKY709 (pdb code 8dey). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2,3) and the Molecular Glue DKY709, PDB code: 8dey:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8dey

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Zinc binding site 1 out of 6 in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2,3) 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(ZF2,3) and the Molecular Glue DKY709 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:152.5
occ:1.00
 SG A:CYS394 2.3 172.2 1.0
SG A:CYS326 2.3 109.7 1.0
SG A:CYS391 2.4 173.5 1.0
SG A:CYS323 2.7 172.8 1.0
CB A:CYS326 2.7 160.8 1.0
CB A:CYS391 3.2 151.1 1.0
CB A:CYS323 3.2 170.9 1.0
CB A:CYS394 3.4 161.6 1.0
N A:CYS326 3.5 166.2 1.0
CA A:CYS326 3.7 169.4 1.0
N A:CYS394 3.8 156.3 1.0
CA A:CYS394 4.1 156.9 1.0
C A:CYS326 4.6 172.2 1.0
N A:GLN327 4.7 177.7 1.0
CB A:ILE393 4.7 132.4 1.0
CA A:CYS323 4.7 162.9 1.0
CA A:CYS391 4.7 143.6 1.0
C A:GLN325 4.7 166.9 1.0
CG2 A:ILE393 4.8 110.6 1.0
C A:ILE393 4.8 153.8 1.0
C A:CYS394 4.8 161.9 1.0
CB A:GLN325 4.9 166.1 1.0
N A:ILE393 5.0 158.4 1.0
N A:ALA395 5.0 162.5 1.0

Zinc binding site 2 out of 6 in 8dey

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Zinc binding site 2 out of 6 in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2,3) 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(ZF2,3) and the Molecular Glue DKY709 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:211.0
occ:1.00
 NE2 C:HIS162 2.0 170.1 1.0
NE2 C:HIS158 2.0 203.1 1.0
SG C:CYS142 2.2 168.1 1.0
CD2 C:HIS158 2.2 204.1 1.0
SG C:CYS145 2.3 169.9 1.0
CD2 C:HIS162 2.7 174.7 1.0
CB C:CYS142 2.9 183.0 1.0
CE1 C:HIS162 2.9 169.9 1.0
CE1 C:HIS158 3.2 194.8 1.0
CG C:HIS158 3.5 203.3 1.0
CB C:CYS145 3.6 166.8 1.0
N C:CYS145 3.8 167.8 1.0
CG C:HIS162 3.8 181.2 1.0
ND1 C:HIS162 3.9 175.2 1.0
ND1 C:HIS158 3.9 199.7 1.0
CA C:CYS145 4.2 167.3 1.0
CA C:CYS142 4.3 183.4 1.0
CB C:ALA147 4.5 173.2 1.0
CB C:GLN144 4.5 175.2 1.0
N C:GLY146 4.5 165.2 1.0
C C:CYS142 4.7 170.9 1.0
N C:ALA147 4.7 166.0 1.0
CB C:HIS158 4.7 197.0 1.0
O C:CYS142 4.8 166.9 1.0
N C:GLN144 4.8 178.9 1.0
C C:CYS145 4.8 170.1 1.0
C C:GLN144 4.9 171.2 1.0
CG2 C:ILE159 4.9 192.8 1.0
O C:HIS158 4.9 192.5 1.0
C C:HIS158 4.9 197.2 1.0
CA C:ILE159 5.0 192.9 1.0
N C:ILE159 5.0 198.4 1.0
CA C:GLN144 5.0 172.0 1.0

Zinc binding site 3 out of 6 in 8dey

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Zinc binding site 3 out of 6 in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2,3) 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(ZF2,3) and the Molecular Glue DKY709 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:243.5
occ:1.00
 NE2 C:HIS186 2.1 209.4 1.0
CD2 C:HIS190 2.2 199.2 1.0
NE2 C:HIS190 2.3 203.9 1.0
SG C:CYS170 2.5 182.4 1.0
SG C:CYS173 2.5 206.4 1.0
CD2 C:HIS186 2.6 204.5 1.0
CB C:CYS170 2.7 194.2 1.0
CE1 C:HIS186 3.2 204.5 1.0
CG C:HIS190 3.5 200.0 1.0
CE1 C:HIS190 3.5 201.0 1.0
CG C:HIS186 3.7 200.4 1.0
ND1 C:HIS186 3.9 203.5 1.0
ND1 C:HIS190 4.1 205.1 1.0
CA C:CYS170 4.2 193.4 1.0
CB C:CYS173 4.2 197.1 1.0
CB C:TYR175 4.3 184.6 1.0
O C:TYR175 4.3 188.2 1.0
CD2 C:LEU187 4.4 163.8 1.0
O C:HIS186 4.6 187.1 1.0
CD2 C:TYR175 4.6 202.3 1.0
CB C:HIS190 4.6 200.5 1.0
N C:TYR175 4.8 183.4 1.0
N C:CYS173 4.8 200.1 1.0
N C:CYS170 4.9 192.4 1.0
C C:HIS186 4.9 190.0 1.0
C C:CYS170 4.9 190.9 1.0
CG C:TYR175 5.0 188.8 1.0
CA C:TYR175 5.0 179.2 1.0
CB C:HIS186 5.0 189.9 1.0

Zinc binding site 4 out of 6 in 8dey

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Zinc binding site 4 out of 6 in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2,3) 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(ZF2,3) and the Molecular Glue DKY709 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:171.4
occ:1.00
 SG D:CYS394 2.3 149.7 1.0
SG D:CYS391 2.4 132.3 1.0
SG D:CYS323 2.4 194.8 1.0
SG D:CYS326 2.8 174.2 1.0
CB D:CYS326 2.8 190.5 1.0
CB D:CYS323 2.9 174.6 1.0
CB D:CYS391 3.0 148.4 1.0
CB D:CYS394 3.5 166.5 1.0
N D:CYS326 3.6 183.4 1.0
CA D:CYS326 3.8 185.6 1.0
N D:CYS394 4.1 169.3 1.0
CA D:CYS394 4.4 161.4 1.0
CA D:CYS323 4.4 167.8 1.0
CA D:CYS391 4.5 152.9 1.0
N D:GLN327 4.7 188.7 1.0
C D:CYS326 4.7 190.1 1.0
C D:GLN325 4.8 183.8 1.0
C D:CYS323 4.9 177.0 1.0
CB D:GLN325 4.9 183.7 1.0
O D:CYS323 4.9 183.8 1.0
C D:CYS394 5.0 155.2 1.0
CB D:ILE393 5.0 175.1 1.0
CB D:SER396 5.0 162.5 1.0

Zinc binding site 5 out of 6 in 8dey

Go back to Zinc Binding Sites List in 8dey
Zinc binding site 5 out of 6 in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2,3) 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 5 of Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2,3) and the Molecular Glue DKY709 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:245.8
occ:1.00
 NE2 F:HIS162 2.0 193.8 1.0
SG F:CYS142 2.3 227.9 1.0
CD2 F:HIS158 2.3 215.3 1.0
NE2 F:HIS158 2.3 217.7 1.0
CD2 F:HIS162 2.4 191.5 1.0
SG F:CYS145 2.4 223.4 1.0
CB F:CYS142 3.0 215.3 1.0
CE1 F:HIS162 3.1 190.2 1.0
CG F:HIS158 3.5 209.4 1.0
CE1 F:HIS158 3.5 207.4 1.0
CG F:HIS162 3.5 196.8 1.0
CB F:CYS145 3.8 183.7 1.0
ND1 F:HIS162 3.8 191.7 1.0
N F:CYS145 4.1 185.4 1.0
ND1 F:HIS158 4.1 207.0 1.0
CG2 F:ILE159 4.4 202.3 1.0
CA F:ILE159 4.4 206.4 1.0
N F:ILE159 4.5 212.8 1.0
CA F:CYS142 4.5 210.7 1.0
CA F:CYS145 4.5 184.5 1.0
CB F:GLN144 4.5 175.5 1.0
C F:HIS158 4.5 208.3 1.0
O F:HIS158 4.5 204.8 1.0
CB F:HIS158 4.6 200.3 1.0
CB F:ALA147 4.6 195.0 1.0
CB F:HIS162 4.8 204.8 1.0
N F:GLY146 4.9 190.8 1.0
CB F:ILE159 4.9 201.6 1.0
N F:ALA147 5.0 199.2 1.0
C F:CYS142 5.0 222.5 1.0

Zinc binding site 6 out of 6 in 8dey

Go back to Zinc Binding Sites List in 8dey
Zinc binding site 6 out of 6 in the Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2,3) 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 6 of Ternary Complex Structure of Cereblon-DDB1 Bound to IKZF2(ZF2,3) and the Molecular Glue DKY709 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn202

b:182.7
occ:1.00
 NE2 F:HIS186 1.9 184.4 1.0
NE2 F:HIS190 2.0 161.0 1.0
SG F:CYS170 2.1 139.4 1.0
CD2 F:HIS190 2.2 161.2 1.0
SG F:CYS173 2.3 139.8 1.0
CD2 F:HIS186 2.6 179.6 1.0
CB F:CYS170 3.0 158.4 1.0
CE1 F:HIS186 3.0 181.5 1.0
CE1 F:HIS190 3.3 148.1 1.0
CG F:HIS190 3.5 146.8 1.0
CB F:CYS173 3.7 152.2 1.0
CG F:HIS186 3.7 180.4 1.0
ND1 F:HIS186 3.9 184.4 1.0
ND1 F:HIS190 4.0 137.4 1.0
N F:CYS173 4.0 155.4 1.0
CA F:CYS170 4.4 160.4 1.0
CA F:CYS173 4.5 156.4 1.0
CB F:PHE172 4.6 145.9 1.0
O F:HIS186 4.6 158.2 1.0
CB F:HIS190 4.7 136.3 1.0
CD2 F:LEU187 4.7 127.0 1.0
C F:CYS170 4.8 165.7 1.0
CD2 F:TYR175 4.9 202.8 1.0
N F:PHE172 4.9 153.0 1.0
O F:CYS170 5.0 169.7 1.0
N F:SER174 5.0 168.5 1.0
CD2 F:PHE172 5.0 143.2 1.0

Reference:

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
Page generated: Fri Aug 22 09:13:27 2025

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