Zinc in PDB 8ou7: Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11D
Protein crystallography data
The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11D, PDB code: 8ou7
was solved by
C.Heim,
L.Bischof,
M.D.Hartmann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.55 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.409,
59.548,
88.413,
90,
90,
90
|
R / Rfree (%)
|
17.6 /
22.4
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11D
(pdb code 8ou7). 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 in Complex with Novel Benzamide-Type Cereblon Binder 11D, PDB code: 8ou7:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 8ou7
Go back to
Zinc Binding Sites List in 8ou7
Zinc binding site 1 out
of 3 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11D
![](/pictures/ZN/pdb/ou/8ou7-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/ou/8ou7-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 in Complex with Novel Benzamide-Type Cereblon Binder 11D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:27.6
occ:1.00
|
HG
|
A:CYS90
|
1.2
|
26.6
|
0.0
|
HG
|
A:CYS24
|
1.2
|
27.2
|
0.0
|
SG
|
A:CYS93
|
2.3
|
28.8
|
1.0
|
SG
|
A:CYS24
|
2.3
|
27.4
|
1.0
|
SG
|
A:CYS27
|
2.3
|
27.7
|
1.0
|
SG
|
A:CYS90
|
2.4
|
26.7
|
1.0
|
HG
|
A:CYS27
|
2.4
|
27.5
|
0.0
|
HG
|
A:CYS93
|
2.5
|
28.7
|
0.0
|
HB3
|
A:CYS24
|
3.0
|
26.2
|
1.0
|
HB3
|
A:CYS90
|
3.1
|
24.8
|
1.0
|
CB
|
A:CYS90
|
3.1
|
24.9
|
1.0
|
H
|
A:CYS93
|
3.1
|
29.3
|
1.0
|
CB
|
A:CYS24
|
3.1
|
26.9
|
1.0
|
HB2
|
A:CYS90
|
3.2
|
24.8
|
1.0
|
HB3
|
A:CYS93
|
3.2
|
27.8
|
1.0
|
HB2
|
A:CYS24
|
3.3
|
26.2
|
1.0
|
CB
|
A:CYS93
|
3.3
|
28.1
|
1.0
|
HB3
|
A:CYS27
|
3.4
|
29.4
|
1.0
|
HB2
|
A:GLN26
|
3.5
|
34.0
|
1.0
|
CB
|
A:CYS27
|
3.5
|
29.7
|
1.0
|
H
|
A:CYS27
|
3.6
|
30.6
|
1.0
|
HB3
|
A:GLN92
|
3.8
|
28.8
|
1.0
|
N
|
A:CYS93
|
3.8
|
30.1
|
1.0
|
HB3
|
A:SER95
|
3.8
|
33.1
|
0.5
|
HB3
|
A:GLN29
|
3.9
|
27.0
|
1.0
|
N
|
A:CYS27
|
4.0
|
28.6
|
1.0
|
HB2
|
A:SER95
|
4.0
|
33.7
|
0.5
|
CA
|
A:CYS93
|
4.0
|
26.1
|
1.0
|
HB2
|
A:CYS93
|
4.1
|
27.8
|
1.0
|
H
|
A:GLN29
|
4.2
|
26.8
|
1.0
|
HB2
|
A:GLN29
|
4.2
|
27.1
|
1.0
|
H
|
A:SER95
|
4.2
|
29.9
|
1.0
|
HB2
|
A:CYS27
|
4.3
|
29.4
|
1.0
|
CA
|
A:CYS27
|
4.3
|
29.9
|
1.0
|
HG
|
A:SER95
|
4.3
|
32.7
|
0.0
|
H
|
A:GLN26
|
4.4
|
27.4
|
1.0
|
CB
|
A:GLN26
|
4.5
|
32.7
|
1.0
|
HD11
|
A:LEU97
|
4.5
|
29.9
|
1.0
|
HB2
|
A:SER95
|
4.5
|
33.1
|
0.5
|
HE21
|
A:GLN92
|
4.5
|
28.1
|
1.0
|
CB
|
A:GLN29
|
4.5
|
26.5
|
1.0
|
H
|
A:GLY28
|
4.6
|
28.6
|
1.0
|
CA
|
A:CYS24
|
4.6
|
23.9
|
1.0
|
H
|
A:GLY94
|
4.6
|
27.8
|
1.0
|
CA
|
A:CYS90
|
4.6
|
23.0
|
1.0
|
H
|
A:GLN92
|
4.6
|
28.6
|
1.0
|
CB
|
A:SER95
|
4.6
|
33.4
|
0.5
|
C
|
A:GLN26
|
4.7
|
36.9
|
1.0
|
CB
|
A:GLN92
|
4.7
|
29.6
|
1.0
|
C
|
A:CYS93
|
4.8
|
29.8
|
1.0
|
HB3
|
A:GLN26
|
4.8
|
34.0
|
1.0
|
HA
|
A:CYS93
|
4.8
|
27.9
|
1.0
|
HG2
|
A:GLN92
|
4.9
|
28.6
|
1.0
|
CB
|
A:SER95
|
4.9
|
34.6
|
0.5
|
HD23
|
A:LEU97
|
4.9
|
31.0
|
1.0
|
C
|
A:CYS27
|
4.9
|
32.3
|
1.0
|
C
|
A:GLN92
|
4.9
|
30.9
|
1.0
|
CA
|
A:GLN26
|
4.9
|
28.5
|
1.0
|
HA
|
A:CYS90
|
4.9
|
23.7
|
1.0
|
N
|
A:GLN26
|
4.9
|
27.4
|
1.0
|
N
|
A:GLY94
|
4.9
|
27.4
|
1.0
|
N
|
A:GLY28
|
5.0
|
27.1
|
1.0
|
OG
|
A:SER95
|
5.0
|
32.7
|
0.5
|
C
|
A:CYS24
|
5.0
|
26.7
|
1.0
|
|
Zinc binding site 2 out
of 3 in 8ou7
Go back to
Zinc Binding Sites List in 8ou7
Zinc binding site 2 out
of 3 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11D
![](/pictures/ZN/pdb/ou/8ou7-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/ou/8ou7-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 in Complex with Novel Benzamide-Type Cereblon Binder 11D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn201
b:33.1
occ:1.00
|
HG
|
B:CYS90
|
1.1
|
30.3
|
0.0
|
HG
|
B:CYS24
|
1.2
|
30.8
|
0.0
|
SG
|
B:CYS90
|
2.3
|
30.5
|
1.0
|
SG
|
B:CYS93
|
2.3
|
33.7
|
1.0
|
SG
|
B:CYS27
|
2.4
|
34.9
|
1.0
|
SG
|
B:CYS24
|
2.4
|
31.1
|
1.0
|
HG
|
B:CYS93
|
2.5
|
33.2
|
0.0
|
HG
|
B:CYS27
|
2.5
|
34.6
|
0.0
|
HB3
|
B:CYS93
|
3.0
|
35.0
|
1.0
|
HB3
|
B:CYS90
|
3.0
|
29.7
|
1.0
|
CB
|
B:CYS90
|
3.1
|
30.9
|
1.0
|
HB3
|
B:CYS24
|
3.1
|
32.0
|
1.0
|
HB2
|
B:CYS90
|
3.1
|
29.7
|
1.0
|
HB3
|
B:CYS27
|
3.1
|
35.3
|
1.0
|
CB
|
B:CYS24
|
3.2
|
33.1
|
1.0
|
CB
|
B:CYS93
|
3.2
|
37.4
|
1.0
|
H
|
B:CYS93
|
3.3
|
32.5
|
1.0
|
HB2
|
B:CYS24
|
3.3
|
32.0
|
1.0
|
H
|
B:CYS27
|
3.3
|
38.1
|
1.0
|
CB
|
B:CYS27
|
3.4
|
35.7
|
1.0
|
HB2
|
B:GLN26
|
3.8
|
39.0
|
1.0
|
N
|
B:CYS27
|
3.8
|
37.7
|
1.0
|
N
|
B:CYS93
|
3.8
|
31.9
|
1.0
|
HB3
|
B:GLN92
|
3.9
|
35.2
|
1.0
|
HB3
|
B:SER95
|
3.9
|
32.2
|
1.0
|
HB2
|
B:CYS93
|
4.0
|
35.0
|
1.0
|
CA
|
B:CYS93
|
4.1
|
30.8
|
1.0
|
H
|
B:GLN29
|
4.1
|
30.6
|
1.0
|
HB2
|
B:CYS27
|
4.1
|
35.3
|
1.0
|
CA
|
B:CYS27
|
4.2
|
34.6
|
1.0
|
H
|
B:SER95
|
4.2
|
30.6
|
1.0
|
HB3
|
B:GLN29
|
4.2
|
37.5
|
1.0
|
HD11
|
B:LEU97
|
4.4
|
30.0
|
1.0
|
H
|
B:GLN92
|
4.5
|
31.7
|
1.0
|
HB2
|
B:GLN29
|
4.5
|
37.5
|
1.0
|
H
|
B:GLY28
|
4.5
|
34.4
|
1.0
|
H
|
B:GLN26
|
4.5
|
36.8
|
1.0
|
HB2
|
B:SER95
|
4.5
|
32.2
|
1.0
|
CA
|
B:CYS90
|
4.6
|
26.4
|
1.0
|
H
|
B:GLY94
|
4.6
|
32.2
|
1.0
|
CA
|
B:CYS24
|
4.6
|
30.3
|
1.0
|
CB
|
B:GLN26
|
4.7
|
36.2
|
1.0
|
CB
|
B:SER95
|
4.7
|
31.2
|
1.0
|
HG2
|
B:GLN92
|
4.7
|
35.9
|
1.0
|
C
|
B:GLN26
|
4.7
|
43.0
|
1.0
|
CB
|
B:GLN92
|
4.8
|
35.4
|
1.0
|
C
|
B:CYS93
|
4.8
|
35.7
|
1.0
|
HE21
|
B:GLN92
|
4.8
|
32.2
|
1.0
|
C
|
B:GLN92
|
4.8
|
35.8
|
1.0
|
C
|
B:CYS27
|
4.8
|
38.8
|
1.0
|
CB
|
B:GLN29
|
4.8
|
35.6
|
1.0
|
HA
|
B:CYS93
|
4.9
|
33.1
|
1.0
|
HA
|
B:CYS90
|
4.9
|
27.8
|
1.0
|
N
|
B:GLY28
|
4.9
|
33.0
|
1.0
|
N
|
B:GLY94
|
4.9
|
31.0
|
1.0
|
HB3
|
B:GLN26
|
4.9
|
39.1
|
1.0
|
HE21
|
B:GLN29
|
5.0
|
47.4
|
1.0
|
HA
|
B:CYS27
|
5.0
|
36.2
|
1.0
|
N
|
B:GLN29
|
5.0
|
31.0
|
1.0
|
|
Zinc binding site 3 out
of 3 in 8ou7
Go back to
Zinc Binding Sites List in 8ou7
Zinc binding site 3 out
of 3 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 11D
![](/pictures/ZN/pdb/ou/8ou7-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/ou/8ou7-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 in Complex with Novel Benzamide-Type Cereblon Binder 11D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn201
b:35.4
occ:1.00
|
HG
|
C:CYS90
|
1.2
|
34.3
|
0.0
|
HG
|
C:CYS24
|
1.2
|
37.0
|
0.0
|
SG
|
C:CYS93
|
2.3
|
38.5
|
1.0
|
SG
|
C:CYS27
|
2.3
|
36.1
|
1.0
|
SG
|
C:CYS90
|
2.4
|
34.6
|
1.0
|
SG
|
C:CYS24
|
2.4
|
37.3
|
1.0
|
HG
|
C:CYS27
|
2.5
|
35.5
|
0.0
|
HG
|
C:CYS93
|
2.5
|
38.1
|
0.0
|
HB3
|
C:CYS24
|
3.1
|
36.8
|
1.0
|
HB3
|
C:CYS90
|
3.1
|
34.8
|
1.0
|
CB
|
C:CYS24
|
3.1
|
36.1
|
1.0
|
CB
|
C:CYS90
|
3.2
|
34.5
|
1.0
|
HB3
|
C:CYS27
|
3.2
|
43.2
|
1.0
|
H
|
C:CYS93
|
3.2
|
34.9
|
1.0
|
HB2
|
C:CYS24
|
3.2
|
36.8
|
1.0
|
HB3
|
C:CYS93
|
3.2
|
37.9
|
1.0
|
HB2
|
C:CYS90
|
3.2
|
34.8
|
1.0
|
CB
|
C:CYS93
|
3.4
|
38.2
|
1.0
|
CB
|
C:CYS27
|
3.4
|
44.8
|
1.0
|
H
|
C:CYS27
|
3.4
|
51.2
|
1.0
|
HB2
|
C:GLN26
|
3.6
|
50.4
|
1.0
|
HB3
|
C:GLN92
|
3.7
|
29.8
|
1.0
|
HB3
|
C:SER95
|
3.7
|
48.6
|
1.0
|
N
|
C:CYS93
|
3.8
|
34.4
|
1.0
|
HB3
|
C:GLN29
|
3.8
|
32.5
|
1.0
|
N
|
C:CYS27
|
3.9
|
51.8
|
1.0
|
H
|
C:GLN29
|
4.0
|
35.5
|
1.0
|
H
|
C:SER95
|
4.0
|
41.9
|
1.0
|
CA
|
C:CYS93
|
4.1
|
36.5
|
1.0
|
CA
|
C:CYS27
|
4.1
|
45.4
|
1.0
|
HB2
|
C:CYS27
|
4.1
|
43.2
|
1.0
|
HB2
|
C:CYS93
|
4.1
|
37.9
|
1.0
|
HB2
|
C:GLN29
|
4.2
|
32.6
|
1.0
|
H
|
C:GLN92
|
4.3
|
32.7
|
1.0
|
H
|
C:GLY28
|
4.4
|
38.5
|
1.0
|
H
|
C:GLY94
|
4.4
|
37.4
|
1.0
|
CB
|
C:GLN29
|
4.5
|
30.6
|
1.0
|
H
|
C:GLN26
|
4.5
|
44.6
|
1.0
|
HD11
|
C:LEU97
|
4.5
|
39.1
|
1.0
|
CB
|
C:GLN26
|
4.6
|
47.7
|
1.0
|
CA
|
C:CYS24
|
4.6
|
38.0
|
1.0
|
CA
|
C:CYS90
|
4.6
|
35.6
|
1.0
|
CB
|
C:GLN92
|
4.6
|
29.9
|
1.0
|
HE21
|
C:GLN92
|
4.7
|
33.2
|
1.0
|
CB
|
C:SER95
|
4.7
|
49.5
|
1.0
|
C
|
C:GLN26
|
4.7
|
57.4
|
1.0
|
C
|
C:CYS27
|
4.7
|
42.0
|
1.0
|
C
|
C:CYS93
|
4.8
|
43.8
|
1.0
|
HD23
|
C:LEU97
|
4.8
|
38.5
|
1.0
|
HG2
|
C:GLN92
|
4.8
|
30.6
|
1.0
|
N
|
C:GLY94
|
4.8
|
33.2
|
1.0
|
N
|
C:GLY28
|
4.8
|
36.3
|
1.0
|
C
|
C:GLN92
|
4.8
|
34.7
|
1.0
|
HB2
|
C:SER95
|
4.8
|
48.6
|
1.0
|
N
|
C:SER95
|
4.9
|
42.2
|
1.0
|
N
|
C:GLN29
|
4.9
|
35.4
|
1.0
|
HA
|
C:CYS93
|
5.0
|
37.6
|
1.0
|
HA
|
C:CYS24
|
5.0
|
37.9
|
1.0
|
HA
|
C:CYS90
|
5.0
|
34.4
|
1.0
|
N
|
C:GLN92
|
5.0
|
31.9
|
1.0
|
HA
|
C:CYS27
|
5.0
|
45.9
|
1.0
|
|
Reference:
C.Steinebach,
A.Bricelj,
A.Murgai,
I.Sosic,
L.Bischof,
Y.L.D.Ng,
C.Heim,
S.Maiwald,
M.Proj,
R.Voget,
F.Feller,
J.Kosmrlj,
V.Sapozhnikova,
A.Schmidt,
M.R.Zuleeg,
P.Lemnitzer,
P.Mertins,
F.K.Hansen,
M.Gutschow,
J.Kronke,
M.D.Hartmann.
Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders For the Design of Protacs. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37902300
DOI: 10.1021/ACS.JMEDCHEM.3C00851
Page generated: Thu Dec 28 13:31:57 2023
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