6R1D

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7d, co-crystallized


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

De-Novo Design of Cereblon (CRBN) Effectors Guided by Natural Hydrolysis Products of Thalidomide Derivatives.

Heim, C.Pliatsika, D.Mousavizadeh, F.Bar, K.Hernandez Alvarez, B.Giannis, A.Hartmann, M.D.

(2019) J Med Chem 62: 6615-6629

  • DOI: 10.1021/acs.jmedchem.9b00454
  • Primary Citation of Related Structures:  
    6R0Q, 6R12, 6R11, 6R0S, 6R13, 6R1K, 6R1A, 6R1D, 6R1C, 6R0U, 6R18, 6R0V, 6R19, 6R1X, 6R1W

  • PubMed Abstract: 
  • Targeted protein degradation via cereblon (CRBN), a substrate receptor of an E3 ubiquitin ligase complex, is an increasingly important strategy in various clinical settings, in which the substrate specificity of CRBN is altered via the binding of small-molecule effectors ...

    Targeted protein degradation via cereblon (CRBN), a substrate receptor of an E3 ubiquitin ligase complex, is an increasingly important strategy in various clinical settings, in which the substrate specificity of CRBN is altered via the binding of small-molecule effectors. To date, such effectors are derived from thalidomide and confer a broad substrate spectrum that is far from being fully characterized. Here, we employed a rational and modular approach to design novel and minimalistic CRBN effectors. In this approach, we took advantage of the binding modes of hydrolyzed metabolites of several thalidomide-derived effectors, which we elucidated via crystallography. These yielded key insights for the optimization of the minimal core binding moiety and its linkage to a chemical moiety that imparts substrate specificity. Based on this scaffold, we present a first active de-novo CRBN effector that is able to degrade the neo-substrate IKZF3 in the cell culture.


    Organizational Affiliation

    Department of Protein Evolution , Max Planck Institute for Developmental Biology , Max-Planck-Ring 5 , 72076 Tübingen , Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cereblon isoform 4A, B125Magnetospirillum gryphiswaldense MSR-1Mutation(s): 0 
Gene Names: MGR_0879
UniProt
Find proteins for A4TVL0 (Magnetospirillum gryphiswaldense)
Explore A4TVL0 
Go to UniProtKB:  A4TVL0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JP5 (Subject of Investigation/LOI)
Query on JP5

Download Ideal Coordinates CCD File 
D [auth A], F [auth B](phenylmethyl) ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate
C12 H12 N2 O4
QRQMHYISDDHZBY-VIFPVBQESA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
JP5 Binding MOAD:  6R1D Ki: 4000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.643α = 90
b = 52.482β = 95.79
c = 59.242γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release