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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 1A1146Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein cereblonB [auth C]381Homo 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
GTEx:  ENSG00000113851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96SW2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LVY
Query on LVY

Download Ideal Coordinates CCD File 
D [auth C]S-Lenalidomide
C13 H13 N3 O3
GOTYRUGSSMKFNF-JTQLQIEISA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LVY BindingDB:  4TZ4 Ki: min: 1490, max: 1.63e+4 (nM) from 2 assay(s)
IC50: min: 1500, max: 3.78e+4 (nM) from 4 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
HKLdata reduction
HKLdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release