8RQ9

Crystal structure of PROTAC CFT-1297 in complex with CRBN-midi and BRD4(BD2)

• PDB DOI: https://doi.org/10.2210/pdb8RQ9/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): Darren, D., Ramachandran, S., Kroupova, A., Zollman, D., Ciulli, A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.293 
• R-Value Work: 0.249 
• R-Value Observed: 0.252 

Starting Models: experimental

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: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 106.86 kDa 
• Atom Count: 6,384 
• Modelled Residue Count: 868 
• Deposited Residue Count: 918 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	A, D [auth C]	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	B, C [auth D]	130	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H2F (Subject of Investigation/LOI)	E [auth A], G [auth C]	(3~{S})-3-[7-[1-[7-[4-[6-(4-chlorophenyl)-1-methyl-spiro[[1,2,4]triazolo[4,3-a][1,4]benzodiazepine-4,1'-cyclopropane]-8-yl]pyrazol-1-yl]heptyl]piperidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]piperidine-2,6-dione C47 H50 Cl N9 O3 SDKKICDYRHTFNX-RWYGWLOXSA-N
ZN	F [auth A], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.293 
• R-Value Work: 0.249 
• R-Value Observed: 0.252 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.882	α = 96.44
b = 52.638	β = 91.49
c = 130.348	γ = 99.22

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2.multiplex	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

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