7SHH | pdb_00007shh

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.216 (Depositor), 0.218 (DCC)
R-Value Work:
0.192 (Depositor), 0.194 (DCC)
R-Value Observed:
0.193 (Depositor)

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Validation slider image for 7SHH

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.1c00650
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 41.92 kDa
Atom Count: 2,557
Modeled Residue Count: 311
Deposited Residue Count: 375
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4TVL0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9FT (Subject of Investigation/LOI) Query on 9FT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C]	E [auth A], G [auth B], I [auth C]	(3R)-3-(4-methoxyphenyl)piperidine-2,6-dione C₁₂ H₁₃ N O₃ UTEUBBDWRDGRCU-SNVBAGLBSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain H [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth C]	D [auth A], F [auth B], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.216 (Depositor), 0.218 (DCC)
R-Value Work: 0.192 (Depositor), 0.194 (DCC)
R-Value Observed: 0.193 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-13

Deposition Author(s):

Nithianantham, S.

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2022-04-13
Type: Initial release
Version 1.1: 2024-05-22
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.