4TZ4

Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history. 


Literature

Structural Basis for Responsiveness to Thalidomide-Analog Drugs Defined by the Crystal Structure of the Human Cereblon:DDB1:Lenalidomide Complex

Chamberlain, P.P., Wang, M., Riley, M., Delker, S., Carmel, G., Miller, K., Lopez-Girona, A., Pagarigan, B., Leon, B., Rychak, E., Corral, L., Lopez-Girona, A., Ren, Y., Wang, M., Riley, M., Delker, S., Ito, T., Hideki, A., Mori, T., Handa, H., Hakoshima, T., Daniel, T.O., Miller, K., Cathers, B.E., Carmel, G., Pagarigan, B., Leon, B., Rychak, E., Corral, L., Ren, Y.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 11,146Homo sapiensMutation(s): 0 
Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblonB [auth C]381Homo sapiensMutation(s): 0 
Gene Names: CRBN, AD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens)
Explore Q96SW2 
Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2
GTEx:  ENSG00000113851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96SW2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
LVY BindingDB:  4TZ4 Ki: min: 1490, max: 1.63e+4 (nM) from 2 assay(s)
IC50: min: 390, max: 3.78e+4 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.862α = 90
b = 129.117β = 90
c = 198.677γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 2.0: 2023-12-27
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 2.1: 2024-04-03
    Changes: Refinement description
  • Version 2.2: 2024-11-20
    Changes: Structure summary