9DJX

Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Optimization of First-in-Class Molecular Glue Degraders of the WIZ Transcription Factor for Fetal Hemoglobin Induction to Treat Sickle Cell Disease.

Kerrigan, J.R.Thomsen, N.M.Cernijenko, A.Kochanek, S.E.Dewhurst, J.O'Brien, G.Ware, N.F.Sanchez, C.C.Manning, J.R.Ma, X.Ornelas, E.Savage, N.A.Partridge, J.R.Patterson, A.W.Lam, P.Dales, N.A.Bonazzi, S.Borikar, S.Hinman, A.E.Ting, P.Y.

(2024) J Med Chem 67: 20682-20694

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02251
  • Primary Citation of Related Structures:  
    9DJT, 9DJX

  • PubMed Abstract: 

    Sickle cell disease (SCD) is a prevalent, life-threatening condition with few treatment options, attributed to a heritable mutation in β-hemoglobin. Therapeutic induction of fetal hemoglobin (HbF) with small molecules has been pursued as a treatment to ameliorate many disease complications but with limited success. Herein, we report the discovery of 10 , a novel, potent, and selective molecular glue degrader of the transcription factor WIZ that robustly induces HbF expression as a potential treatment for SCD. 10 was optimized from a phenotypic screening hit utilizing insights from X-ray crystallography and computational modeling to improve potency, selectivity and in vivo exposure. In an hNBSGW mouse xenograft model, 10 demonstrated robust WIZ degradation and HbF induction. These results highlight the potential of WIZ degraders as a promising therapy for sickle cell disease.


  • Organizational Affiliation

    Novartis Biomedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon
A, D
373Homo sapiensMutation(s): 0 
Gene Names: CRBN
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens)
Explore Q96SW2 
Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2
GTEx:  ENSG00000113851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96SW2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1
B, E
836Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Wiz
C, F
30Homo sapiensMutation(s): 0 
Gene Names: WIZZNF803
UniProt & NIH Common Fund Data Resources
Find proteins for O95785 (Homo sapiens)
Explore O95785 
Go to UniProtKB:  O95785
PHAROS:  O95785
GTEx:  ENSG00000011451 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95785
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A5I (Subject of Investigation/LOI)
Query on A1A5I

Download Ideal Coordinates CCD File 
I [auth A],
M [auth D]
(3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione
C21 H27 N3 O4
IHBGNCYMSRWSLK-XCRHUMRWSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
L [auth D],
N [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
J [auth C],
K [auth D],
O [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.114α = 90
b = 145.029β = 90
c = 191.895γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2024-12-11
    Changes: Database references