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 1.3 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
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblonA [auth C],
B [auth A],
C [auth B],
D
108Mus 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8C7D2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EF2
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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
L [auth B]
M [auth B]
N [auth B]
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
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
Binding Affinity Annotations 
IDSourceBinding Affinity
EF2 BindingDB:  4TZC Ki: min: 8510, max: 2.27e+4 (nM) from 2 assay(s)
IC50: min: 268, max: 2.99e+4 (nM) from 6 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

View Full Validation Report



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
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references