8RQ8

Crystal structure of CRBN-midi in complex with mezigdomide

• PDB DOI: https://doi.org/10.2210/pdb8RQ8/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-01-17 Released: 2024-09-25 
• Deposition Author(s): Zollman, D., Kroupova, A., Pethe, J., Ciulli, A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.285 
• R-Value Work: 0.258 
• R-Value Observed: 0.259 

Starting Model: in silico

Literature

Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders

Kroupova, A., Zollman, D., Ciulli, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.11 kDa 
• Atom Count: 2,480 
• Modelled Residue Count: 312 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	A	329	Homo sapiens	Mutation(s): 12  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QFC (Subject of Investigation/LOI)	C [auth A]	Mezigdomide C32 H30 F N5 O4 YTINZZFBHWSAGL-NDEPHWFRSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.285 
• R-Value Work: 0.258 
• R-Value Observed: 0.259 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.046	α = 90
b = 51.046	β = 90
c = 267.677	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Zollman, D., Kroupova, A., Pethe, J., Ciulli, A.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release