4TZC

Crystal Structure of Murine Cereblon in Complex with Thalidomide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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.Lopez-Girona, A.Miller, K.Carmel, G.Pagarigan, B.Leon, B.Rychak, E.Corral, L.Ren, Y.Wang, M.Riley, M.Delker, S.Ito, T.Hideki, A.Mori, T.Hirano, Y.Handa, H.Hakoshima, T.Daniel, T.O.Cathers, B.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein cereblonB [auth A], C [auth B], A [auth C], D108Mus musculusMutation(s): 0 
Gene Names: Crbn
UniProt & NIH Common Fund Data Resources
Find proteins for Q8C7D2 (Mus musculus)
Explore Q8C7D2 
Go to UniProtKB:  Q8C7D2
IMPC:  MGI:1913277
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EF2 (Subject of Investigation/LOI)
Query on EF2

Download Ideal Coordinates CCD File 
F [auth C], J [auth A], O [auth B], T [auth D]S-Thalidomide
C13 H10 N2 O4
UEJJHQNACJXSKW-VIFPVBQESA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], Q [auth D], R [auth D], S [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth C], G [auth A], K [auth B], P [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EF2 BindingDB:  4TZC Ki: 2.27e+4 (nM) from 1 assay(s)
IC50: min: 1.00e+4, max: 2.99e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.146α = 90
b = 143.146β = 90
c = 143.146γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata 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
  • Version 1.1: 2016-03-16
    Changes: Data collection
  • Version 1.2: 2017-09-27
    Changes: Derived calculations, Refinement description