6R18

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 11a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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, 6R0S, 6R0U, 6R0V, 6R11, 6R12, 6R13, 6R18, 6R19, 6R1A, 6R1C, 6R1D, 6R1K, 6R1W, 6R1X

  • 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cereblon isoform 4A, B, C125Magnetospirillum gryphiswaldense MSR-1Mutation(s): 0 
Gene Names: MGR_0879
UniProt
Find proteins for A4TVL0 (Magnetospirillum gryphiswaldense)
Explore A4TVL0 
Go to UniProtKB:  A4TVL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4TVL0
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cereblon isoform 4D3Magnetospirillum gryphiswaldense MSR-1Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JOQ
Query on JOQ

Download Ideal Coordinates CCD File 
I [auth B][4-(aminomethyl)phenyl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate
C13 H15 N3 O4
PPHDAIUDWPTCMT-JTQLQIEISA-N
 Ligand Interaction
EF2
Query on EF2

Download Ideal Coordinates CCD File 
F [auth A],
M [auth C]
S-Thalidomide
C13 H10 N2 O4
UEJJHQNACJXSKW-VIFPVBQESA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EF2 BindingDB:  6R18 Ki: 4400 (nM) from 1 assay(s)
IC50: 7800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.63α = 90
b = 59.592β = 90
c = 88.894γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection