Zinc in PDB 8ou3: Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D

Protein crystallography data

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D, PDB code: 8ou3 was solved by C.Heim, L.Bischof, S.Maiwald, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.33 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.793, 59.519, 88.149, 90, 90, 90
R / Rfree (%) 21.5 / 23.8

Other elements in 8ou3:

The structure of Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D also contains other interesting chemical elements:

Fluorine (F) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D (pdb code 8ou3). 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 8D, PDB code: 8ou3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8ou3

Go back to Zinc Binding Sites List in 8ou3
Zinc binding site 1 out of 3 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D


Mono view


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 8D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:21.5
occ:1.00
SG A:CYS24 2.3 20.9 1.0
SG A:CYS93 2.3 22.2 1.0
SG A:CYS27 2.3 22.2 1.0
SG A:CYS90 2.4 21.2 1.0
CB A:CYS24 3.1 19.7 1.0
CB A:CYS90 3.2 20.4 1.0
CB A:CYS93 3.3 20.5 1.0
CB A:CYS27 3.5 23.6 1.0
N A:CYS93 3.8 22.2 1.0
N A:CYS27 3.9 22.7 1.0
CA A:CYS93 4.1 22.4 1.0
CA A:CYS27 4.2 23.6 1.0
CB A:SER95 4.4 23.7 1.0
CA A:CYS24 4.5 19.0 1.0
CB A:GLN26 4.5 26.8 1.0
CB A:GLN29 4.6 21.4 1.0
CA A:CYS90 4.6 19.8 1.0
C A:GLN26 4.6 26.9 1.0
C A:CYS93 4.8 22.4 1.0
CB A:GLN92 4.8 23.7 1.0
N A:GLN26 4.8 21.9 1.0
N A:GLY94 4.9 21.7 1.0
C A:GLN92 4.9 22.3 1.0
C A:CYS27 4.9 24.1 1.0
CA A:GLN26 4.9 24.9 1.0
N A:SER95 4.9 21.5 1.0
N A:GLY28 4.9 21.6 1.0
C A:CYS24 4.9 21.0 1.0

Zinc binding site 2 out of 3 in 8ou3

Go back to Zinc Binding Sites List in 8ou3
Zinc binding site 2 out of 3 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D


Mono view


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 8D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:26.5
occ:1.00
SG B:CYS93 2.3 28.6 1.0
SG B:CYS90 2.3 25.8 1.0
SG B:CYS24 2.4 26.0 1.0
SG B:CYS27 2.4 28.1 1.0
CB B:CYS90 3.1 24.8 1.0
CB B:CYS24 3.2 27.2 1.0
CB B:CYS93 3.3 30.0 1.0
CB B:CYS27 3.3 29.6 1.0
N B:CYS27 3.8 28.5 1.0
N B:CYS93 3.8 26.2 1.0
CA B:CYS93 4.1 27.9 1.0
CA B:CYS27 4.1 29.1 1.0
CA B:CYS90 4.6 22.9 1.0
CA B:CYS24 4.6 23.4 1.0
CB B:GLN92 4.7 26.5 1.0
CB B:SER95 4.7 27.7 1.0
C B:GLN26 4.7 30.7 1.0
C B:GLN92 4.7 25.4 1.0
C B:CYS27 4.7 28.7 1.0
C B:CYS93 4.8 29.1 1.0
CB B:GLN26 4.8 33.6 1.0
N B:GLY28 4.8 26.9 1.0
CB B:GLN29 4.9 30.8 1.0
N B:GLY94 4.9 29.6 1.0
N B:GLN29 5.0 27.9 1.0

Zinc binding site 3 out of 3 in 8ou3

Go back to Zinc Binding Sites List in 8ou3
Zinc binding site 3 out of 3 in the Cereblon Isoform 4 in Complex with Novel Benzamide-Type Cereblon Binder 8D


Mono view


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 8D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:26.0
occ:1.00
SG C:CYS27 2.3 26.9 1.0
SG C:CYS93 2.3 27.1 1.0
SG C:CYS24 2.3 27.3 1.0
SG C:CYS90 2.4 25.6 1.0
CB C:CYS24 3.1 27.2 1.0
CB C:CYS90 3.2 25.6 1.0
CB C:CYS93 3.3 25.6 1.0
CB C:CYS27 3.4 31.5 1.0
N C:CYS93 3.8 25.2 1.0
N C:CYS27 3.8 31.5 1.0
CA C:CYS93 4.1 26.4 1.0
CA C:CYS27 4.1 32.1 1.0
CB C:GLN29 4.5 24.9 1.0
CB C:SER95 4.5 28.8 1.0
CA C:CYS24 4.6 28.4 1.0
CB C:GLN26 4.6 37.7 1.0
CA C:CYS90 4.6 25.9 1.0
CB C:GLN92 4.6 24.3 1.0
C C:GLN26 4.7 36.0 1.0
C C:CYS93 4.7 27.4 1.0
C C:CYS27 4.7 32.0 1.0
N C:GLY28 4.8 28.0 1.0
C C:GLN92 4.8 25.4 1.0
N C:GLY94 4.8 28.8 1.0
N C:GLN29 4.8 26.9 1.0
N C:SER95 4.9 27.8 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 Oct 31 08:57:57 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy