7SHH

Bacterial cereblon homologue in complex with (R)-3-(4-methoxyphenyl)piperidine-2,6-dione

• PDB DOI: https://doi.org/10.2210/pdb7SHH/pdb

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


• Deposited: 2021-10-08 Released: 2022-04-13 
• Deposition Author(s): Nithianantham, S., Fischer, M.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Development of Potent and Selective Janus Kinase 2/3 Directing PG-PROTACs.

Alcock, L.J., Chang, Y., Jarusiewicz, J.A., Actis, M., Nithianantham, S., Mayasundari, A., Min, J., Maxwell, D., Hunt, J., Smart, B., Yang, J.J., Nishiguchi, G., Fischer, M., Mullighan, C.G., Rankovic, Z.

(2022) ACS Med Chem Lett 13: 475-482

• PubMed: 35300081 
• DOI: https://doi.org/10.1021/acsmedchemlett.1c00650
• Primary Citation of Related Structures:  
  7SHH


• PubMed Abstract: 
  

  Aberrant activation of the JAK-STAT signaling pathway has been implicated in the pathogenesis of a range of hematological malignancies and autoimmune disorders. Here we describe the design, synthesis, and characterization of JAK2/3 PROTACs utilizing a phenyl glutarimide (PG) ligand as the cereblon (CRBN) recruiter. SJ10542 displayed high selectivity over GSPT1 and other members of the JAK family and potency in patient-derived ALL cells containing both JAK2 fusions and CRLF2 rearrangements.

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Organizational Affiliation: 

Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.

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: 41.92 kDa 
• Atom Count: 2,557 
• Modelled Residue Count: 311 
• 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	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
9FT (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C]	(3R)-3-(4-methoxyphenyl)piperidine-2,6-dione C12 H13 N O3 UTEUBBDWRDGRCU-SNVBAGLBSA-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: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.311	α = 90
b = 59.586	β = 90
c = 87.706	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-13 
Deposition Author(s): Nithianantham, S., Fischer, M.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2022-04-13
  Type: Initial release