4TZU

Crystal Structure of Murine Cereblon in Complex with Pomalidomide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 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.Ito, T.Hideki, A.Mori, T.Handa, H.Hakoshima, T.Daniel, T.O.Cathers, B.E.Lopez-Girona, A.Miller, K.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
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon
A, B, C, 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
Y70
Query on Y70

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
Q [auth C],
T [auth D]
S-Pomalidomide
C13 H11 N3 O4
UVSMNLNDYGZFPF-QMMMGPOBSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
I [auth B]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B],
N [auth C],
O [auth C],
R [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
P [auth C],
S [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.34α = 90
b = 143.34β = 90
c = 143.34γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

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 2.0: 2017-09-27
    Changes: Atomic model, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Refinement description