5HXB

Cereblon in complex with DDB1, CC-885, and GSPT1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A novel cereblon modulator recruits GSPT1 to the CRL4(CRBN) ubiquitin ligase.

Matyskiela, M.E.Lu, G.Ito, T.Pagarigan, B.Lu, C.C.Miller, K.Fang, W.Wang, N.Y.Nguyen, D.Houston, J.Carmel, G.Tran, T.Riley, M.Nosaka, L.Lander, G.C.Gaidarova, S.Xu, S.Ruchelman, A.L.Handa, H.Carmichael, J.Daniel, T.O.Cathers, B.E.Lopez-Girona, A.Chamberlain, P.P.

(2016) Nature 535: 252-257

  • DOI: 10.1038/nature18611
  • Primary Citation of Related Structures:  
    5HXB

  • PubMed Abstract: 
  • Immunomodulatory drugs bind to cereblon (CRBN) to confer differentiated substrate specificity on the CRL4(CRBN) E3 ubiquitin ligase. Here we report the identification of a new cereblon modulator, CC-885, with potent anti-tumour activity. The anti-tum ...

    Immunomodulatory drugs bind to cereblon (CRBN) to confer differentiated substrate specificity on the CRL4(CRBN) E3 ubiquitin ligase. Here we report the identification of a new cereblon modulator, CC-885, with potent anti-tumour activity. The anti-tumour activity of CC-885 is mediated through the cereblon-dependent ubiquitination and degradation of the translation termination factor GSPT1. Patient-derived acute myeloid leukaemia tumour cells exhibit high sensitivity to CC-885, indicating the clinical potential of this mechanism. Crystallographic studies of the CRBN-DDB1-CC-885-GSPT1 complex reveal that GSPT1 binds to cereblon through a surface turn containing a glycine residue at a key position, interacting with both CC-885 and a 'hotspot' on the cereblon surface. Although GSPT1 possesses no obvious structural, sequence or functional homology to previously known cereblon substrates, mutational analysis and modelling indicate that the cereblon substrate Ikaros uses a similar structural feature to bind cereblon, suggesting a common motif for substrate recruitment. These findings define a structural degron underlying cereblon 'neosubstrate' selectivity, and identify an anti-tumour target rendered druggable by cereblon modulation.


    Organizational Affiliation

    Celgene Corporation, 10300 Campus Point Drive, Suite 100, San Diego, California 92121, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic peptide chain release factor GTP-binding subunit ERF3AAX199Homo sapiensMutation(s): 0 
Gene Names: GSPT1ERF3A
Find proteins for P15170 (Homo sapiens)
Explore P15170 
Go to UniProtKB:  P15170
NIH Common Fund Data Resources
PHAROS  P15170
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 1BY1140Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
NIH Common Fund Data Resources
PHAROS  Q16531
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein cereblonCZ406Homo sapiensMutation(s): 0 
Gene Names: CRBNAD-006
Find proteins for Q96SW2 (Homo sapiens)
Explore Q96SW2 
Go to UniProtKB:  Q96SW2
NIH Common Fund Data Resources
PHAROS  Q96SW2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
85C
Query on 85C

Download CCD File 
C, Z
1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea
C22 H21 Cl N4 O4
DOEVCIHTTTYVCC-SFHVURJKSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
C, Z
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.747α = 90
b = 111.522β = 95.81
c = 175.057γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-07-06
    Changes: Database references
  • Version 1.2: 2016-07-27
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations