Zinc in PDB 8aop: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R
Protein crystallography data
The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R, PDB code: 8aop
was solved by
S.Maiwald,
C.Heim,
M.D.Hartmann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.70 /
1.94
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.79,
59.194,
87.861,
90,
90,
90
|
R / Rfree (%)
|
19.7 /
22.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R
(pdb code 8aop). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R, PDB code: 8aop:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 8aop
Go back to
Zinc Binding Sites List in 8aop
Zinc binding site 1 out
of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R
![](/pictures/ZN/pdb/ao/8aop-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/ao/8aop-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:38.9
occ:1.00
|
SG
|
A:CYS24
|
2.3
|
36.2
|
1.0
|
SG
|
A:CYS93
|
2.3
|
39.9
|
1.0
|
SG
|
A:CYS90
|
2.3
|
38.4
|
1.0
|
SG
|
A:CYS27
|
2.3
|
42.0
|
1.0
|
CB
|
A:CYS90
|
3.1
|
39.3
|
1.0
|
CB
|
A:CYS24
|
3.1
|
36.5
|
1.0
|
CB
|
A:CYS93
|
3.3
|
41.5
|
1.0
|
CB
|
A:CYS27
|
3.4
|
43.0
|
1.0
|
N
|
A:CYS93
|
3.8
|
40.5
|
1.0
|
N
|
A:CYS27
|
3.9
|
39.9
|
1.0
|
CA
|
A:CYS93
|
4.1
|
41.4
|
1.0
|
CA
|
A:CYS27
|
4.2
|
42.0
|
1.0
|
CB
|
A:SER95
|
4.5
|
40.5
|
1.0
|
CB
|
A:GLN29
|
4.5
|
39.4
|
0.5
|
CB
|
A:GLN26
|
4.5
|
47.1
|
1.0
|
CA
|
A:CYS90
|
4.5
|
38.9
|
1.0
|
CA
|
A:CYS24
|
4.5
|
35.7
|
1.0
|
CB
|
A:GLN29
|
4.6
|
41.8
|
0.5
|
C
|
A:GLN26
|
4.6
|
42.6
|
1.0
|
CB
|
A:GLN92
|
4.7
|
40.5
|
1.0
|
C
|
A:CYS93
|
4.8
|
41.2
|
1.0
|
C
|
A:CYS27
|
4.9
|
41.9
|
1.0
|
N
|
A:GLN26
|
4.9
|
39.8
|
1.0
|
CA
|
A:GLN26
|
4.9
|
44.6
|
1.0
|
C
|
A:GLN92
|
4.9
|
41.3
|
1.0
|
N
|
A:SER95
|
4.9
|
39.4
|
1.0
|
N
|
A:GLY94
|
4.9
|
40.9
|
1.0
|
C
|
A:CYS24
|
5.0
|
36.8
|
1.0
|
N
|
A:GLY28
|
5.0
|
39.3
|
1.0
|
|
Zinc binding site 2 out
of 3 in 8aop
Go back to
Zinc Binding Sites List in 8aop
Zinc binding site 2 out
of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R
![](/pictures/ZN/pdb/ao/8aop-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/ao/8aop-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn201
b:68.5
occ:1.00
|
SG
|
B:CYS90
|
2.3
|
65.5
|
1.0
|
SG
|
B:CYS24
|
2.4
|
62.9
|
1.0
|
SG
|
B:CYS27
|
2.4
|
72.9
|
1.0
|
SG
|
B:CYS93
|
2.4
|
72.1
|
1.0
|
CB
|
B:CYS90
|
3.0
|
57.5
|
1.0
|
CB
|
B:CYS24
|
3.1
|
59.5
|
1.0
|
CB
|
B:CYS27
|
3.3
|
75.4
|
1.0
|
CB
|
B:CYS93
|
3.5
|
73.7
|
1.0
|
N
|
B:CYS27
|
3.9
|
72.6
|
1.0
|
N
|
B:CYS93
|
3.9
|
70.1
|
1.0
|
CA
|
B:CYS27
|
4.1
|
74.9
|
1.0
|
CA
|
B:CYS93
|
4.2
|
72.3
|
1.0
|
CA
|
B:CYS90
|
4.4
|
53.3
|
1.0
|
CB
|
B:GLN92
|
4.5
|
71.0
|
1.0
|
CA
|
B:CYS24
|
4.6
|
55.6
|
1.0
|
C
|
B:GLN26
|
4.7
|
75.5
|
1.0
|
CB
|
B:GLN26
|
4.8
|
77.2
|
1.0
|
C
|
B:CYS27
|
4.8
|
71.7
|
1.0
|
C
|
B:GLN92
|
4.9
|
72.1
|
1.0
|
CB
|
B:GLN29
|
4.9
|
66.7
|
1.0
|
CB
|
B:SER95
|
4.9
|
57.9
|
1.0
|
C
|
B:CYS93
|
4.9
|
69.0
|
1.0
|
N
|
B:GLY28
|
4.9
|
66.8
|
1.0
|
C
|
B:CYS90
|
5.0
|
54.6
|
1.0
|
N
|
B:GLY94
|
5.0
|
66.2
|
1.0
|
|
Zinc binding site 3 out
of 3 in 8aop
Go back to
Zinc Binding Sites List in 8aop
Zinc binding site 3 out
of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R
![](/pictures/ZN/pdb/ao/8aop-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/ao/8aop-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 14R within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn201
b:58.1
occ:1.00
|
SG
|
C:CYS24
|
2.3
|
63.1
|
1.0
|
SG
|
C:CYS90
|
2.3
|
58.9
|
1.0
|
SG
|
C:CYS27
|
2.3
|
58.3
|
1.0
|
SG
|
C:CYS93
|
2.4
|
60.6
|
1.0
|
CB
|
C:CYS24
|
3.1
|
62.8
|
1.0
|
CB
|
C:CYS90
|
3.2
|
61.9
|
1.0
|
CB
|
C:CYS27
|
3.3
|
60.3
|
1.0
|
CB
|
C:CYS93
|
3.4
|
60.1
|
1.0
|
N
|
C:CYS27
|
3.7
|
65.2
|
1.0
|
N
|
C:CYS93
|
3.8
|
59.6
|
1.0
|
CA
|
C:CYS27
|
4.1
|
62.1
|
1.0
|
CA
|
C:CYS93
|
4.1
|
60.4
|
1.0
|
CB
|
C:GLN29
|
4.4
|
59.1
|
1.0
|
CB
|
C:GLN26
|
4.5
|
71.9
|
1.0
|
CB
|
C:SER95
|
4.6
|
70.0
|
1.0
|
CB
|
C:GLN92
|
4.6
|
55.5
|
1.0
|
N
|
C:GLY28
|
4.6
|
61.4
|
1.0
|
CA
|
C:CYS24
|
4.6
|
65.0
|
1.0
|
CA
|
C:CYS90
|
4.6
|
63.0
|
1.0
|
C
|
C:CYS27
|
4.7
|
62.0
|
1.0
|
C
|
C:GLN26
|
4.7
|
67.7
|
1.0
|
C
|
C:GLN92
|
4.8
|
57.1
|
1.0
|
C
|
C:CYS93
|
4.8
|
62.6
|
1.0
|
N
|
C:GLN29
|
4.8
|
59.8
|
1.0
|
N
|
C:GLY94
|
4.8
|
64.1
|
1.0
|
N
|
C:SER95
|
4.9
|
68.4
|
1.0
|
CA
|
C:GLN26
|
5.0
|
70.0
|
1.0
|
N
|
C:GLN26
|
5.0
|
69.2
|
1.0
|
|
Reference:
M.Krasavin,
M.Adamchik,
A.Bubyrev,
C.Heim,
S.Maiwald,
D.Zhukovsky,
P.Zhmurov,
A.Bunev,
M.D.Hartmann.
Synthesis of Novel Glutarimide Ligands For the E3 Ligase Substrate Receptor Cereblon (Crbn): Investigation of Their Binding Mode and Antiproliferative Effects Against Myeloma Cell Lines. Eur.J.Med.Chem. V. 246 14990 2023.
ISSN: ISSN 0223-5234
PubMed: 36476642
DOI: 10.1016/J.EJMECH.2022.114990
Page generated: Sat Apr 8 07:44:22 2023
|