5YJ1

Mouse Cereblon thalidomide binding domain complexed with R-form thalidomide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of thalidomide enantiomer binding to cereblon

Mori, T.Ito, T.Liu, S.Ando, H.Sakamoto, S.Yamaguchi, Y.Tokunaga, E.Shibata, N.Handa, H.Hakoshima, T.

(2018) Sci Rep 8: 1294-1294

  • DOI: 10.1038/s41598-018-19202-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thalidomide possesses two optical isomers which have been reported to exhibit different pharmacological and toxicological activities. However, the precise mechanism by which the two isomers exert their different activities remains poorly understood. ...

    Thalidomide possesses two optical isomers which have been reported to exhibit different pharmacological and toxicological activities. However, the precise mechanism by which the two isomers exert their different activities remains poorly understood. Here, we present structural and biochemical studies of (S)- and (R)-enantiomers bound to the primary target of thalidomide, cereblon (CRBN). Our biochemical studies employed deuterium-substituted thalidomides to suppress optical isomer conversion, and established that the (S)-enantiomer exhibited ~10-fold stronger binding to CRBN and inhibition of self-ubiquitylation compared to the (R)-enantiomer. The crystal structures of the thalidomide-binding domain of CRBN bound to each enantiomer show that both enantiomers bind the tri-Trp pocket, although the bound form of the (S)-enantiomer exhibited a more relaxed glutarimide ring conformation. The (S)-enantiomer induced greater teratogenic effects on fins of zebrafish compared to the (R)-enantiomer. This study has established a mechanism by which thalidomide exerts its effects in a stereospecific manner at the atomic level.


    Organizational Affiliation

    Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein cereblon
A, D, G, J, M, P, S, V, Y, b, e, h, k, n, q, t
111Mus musculusMutation(s): 0 
Gene Names: Crbn
Find proteins for Q8C7D2 (Mus musculus)
Go to UniProtKB:  Q8C7D2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, b, D, e, G, h, J, k, M, n, P, q, S, t, V, Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, b, D, e, h, J, k, M, n, P, q, S, t, V, Y
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
6EL
Query on 6EL

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Download CCD File 
A, b, D, e, G, h, J, k, M, n, P, q, S, t, V, Y
2-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]isoindole-1,3-dione
C13 H10 N2 O4
UEJJHQNACJXSKW-SECBINFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.199 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 201.615α = 90.00
b = 201.615β = 90.00
c = 123.572γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Structure summary