5FQD

Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural Basis of Lenalidomide-Induced Ck1Alpha Degradation by the Crl4(Crbn) Ubiquitin Ligase.

Petzold, G.Fischer, E.S.Thoma, N.H.

(2016) Nature 532: 127

  • DOI: 10.1038/nature16979
  • Primary Citation of Related Structures:  
    5FQD

  • PubMed Abstract: 
  • Thalidomide and its derivatives, lenalidomide and pomalidomide, are immune modulatory drugs (IMiDs) used in the treatment of haematologic malignancies. IMiDs bind CRBN, the substrate receptor of the CUL4-RBX1-DDB1-CRBN (also known as CRL4(CRBN)) E3 ubiquitin ligase, and inhibit ubiquitination of endogenous CRL4(CRBN) substrates ...

    Thalidomide and its derivatives, lenalidomide and pomalidomide, are immune modulatory drugs (IMiDs) used in the treatment of haematologic malignancies. IMiDs bind CRBN, the substrate receptor of the CUL4-RBX1-DDB1-CRBN (also known as CRL4(CRBN)) E3 ubiquitin ligase, and inhibit ubiquitination of endogenous CRL4(CRBN) substrates. Unexpectedly, IMiDs also repurpose the ligase to target new proteins for degradation. Lenalidomide induces degradation of the lymphoid transcription factors Ikaros and Aiolos (also known as IKZF1 and IKZF3), and casein kinase 1α (CK1α), which contributes to its clinical efficacy in the treatment of multiple myeloma and 5q-deletion associated myelodysplastic syndrome (del(5q) MDS), respectively. How lenalidomide alters the specificity of the ligase to degrade these proteins remains elusive. Here we present the 2.45 Å crystal structure of DDB1-CRBN bound to lenalidomide and CK1α. CRBN and lenalidomide jointly provide the binding interface for a CK1α β-hairpin-loop located in the kinase N-lobe. We show that CK1α binding to CRL4(CRBN) is strictly dependent on the presence of an IMiD. Binding of IKZF1 to CRBN similarly requires the compound and both, IKZF1 and CK1α, use a related binding mode. Our study provides a mechanistic explanation for the selective efficacy of lenalidomide in del(5q) MDS therapy. We anticipate that high-affinity protein-protein interactions induced by small molecules will provide opportunities for drug development, particularly for targeted protein degradation.


    Organizational Affiliation

    University of Basel, Petersplatz 10, CH-4003 Basel, Switzerland.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA DAMAGE-BINDING PROTEIN 1A, D856Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
EC: 6.3.2.19
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
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Go to UniProtKB:  Q16531
PHAROS:  Q16531
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN CEREBLONB, E426Homo sapiensMutation(s): 0 
Gene Names: CRBNAD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens)
Explore Q96SW2 
Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CASEIN KINASE I ISOFORM ALPHAC, F341Homo sapiensMutation(s): 0 
Gene Names: CSNK1A1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P48729 (Homo sapiens)
Explore P48729 
Go to UniProtKB:  P48729
PHAROS:  P48729
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LVY (Subject of Investigation/LOI)
Query on LVY

Download Ideal Coordinates CCD File 
H [auth B], J [auth E]S-Lenalidomide
C13 H13 N3 O3
GOTYRUGSSMKFNF-JTQLQIEISA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth B], I [auth E]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LVY BindingDB:  5FQD Ki: 1490 (nM) from 1 assay(s)
IC50: min: 1500, max: 3000 (nM) from 3 assay(s)
Binding MOAD:  5FQD Kd: 242 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.97α = 106.02
b = 109.93β = 93.19
c = 112.4γ = 101.63
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2016-04-13
    Changes: Database references
  • Version 1.3: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy