7PJK | pdb_00007pjk

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with a benzotriazole analog of thalidomide

• PDB DOI: https://doi.org/10.2210/pdb7PJK/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Magnetospirillum gryphiswaldense MSR-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-08-24 Released: 2022-03-16 
• Deposition Author(s): Heim, C., Hartmann, M.D., Maiwald, S.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Replacing the phthalimide core in thalidomide with benzotriazole.

Krasavin, M., Bubyrev, A., Kazantsev, A., Heim, C., Maiwald, S., Zhukovsky, D., Dar'in, D., Hartmann, M.D., Bunev, A.

(2022) J Enzyme Inhib Med Chem 37: 527-530

• PubMed: 35220840 
• DOI: https://doi.org/10.1080/14756366.2021.2024525
• Primary Citation Related Structures: 
  7PJK


• PubMed Abstract: 
  

  The advent of proteolysis-targeting chimaeras (PROTACs) mandates that new ligands for the recruitment of E3 ligases are discovered. The traditional immunomodulatory drugs (IMiDs) such as thalidomide and its analogues (all based on the phthalimide glutarimide core) bind to Cereblon, the substrate receptor of the CRL4A ^CRBN E3 ligase. We designed a thalidomide analogue in which the phthalimide moiety was replaced with benzotriazole, using an innovative synthesis strategy. Compared to thalidomide, the resulting "benzotriazolo thalidomide" has a similar binding mode, but improved properties, as revealed in crystallographic analyses, affinity assays and cell culture.

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Organizational Affiliation: 
• Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia.
Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
Medicinal Chemistry Center, Togliatti State University, Togliatti, Russia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.77 kDa 
• Atom Count: 2,168 
• Modeled Residue Count: 265 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cereblon isoform 4	A, B, C	125	Magnetospirillum gryphiswaldense MSR-1	Mutation(s): 0  Gene Names: MGR_0879
UniProt
Find proteins for A4TVL0 (Magnetospirillum gryphiswaldense) Explore A4TVL0  Go to UniProtKB:  A4TVL0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7SE (Subject of Investigation/LOI)	E [auth A], G [auth B]	(3S)-3-(benzotriazol-2-yl)piperidine-2,6-dione C11 H10 N4 O2 QFGWCBAWFMYBCK-VIFPVBQESA-N
ZN	D [auth A], F [auth B], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.779	α = 90
b = 59.435	β = 90
c = 88.189	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Heim, C., Hartmann, M.D., Maiwald, S.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description