9DOM | pdb_00009dom

PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.234 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

Development of PVTX-405 as a potent and highly selective molecular glue degrader of IKZF2 for cancer immunotherapy.

Chen, Z.Dhruv, H.Zhang, X.Rej, R.K.Bai, L.McEachern, D.Kirchhoff, P.Nagilla, R.Jolivette, L.J.Rice, C.T.Orth, P.Strickland, C.O.Priestley, E.S.Mohammad, H.P.Wang, M.Wen, B.Sun, D.Sui, Z.Wang, S.

(2025) Nat Commun 16: 4095-4095

  • DOI: https://doi.org/10.1038/s41467-025-58431-z
  • Primary Citation of Related Structures:  
    9DOM

  • PubMed Abstract: 

    IKZF2 (Helios) is a transcription factor that is selectively expressed by Tregs and is essential for preserving the function and stability of Tregs in the tumor microenvironment (TME), where it suppresses the anti-tumor immune response. Targeted IKZF2 degradation by small molecules represents a promising strategy for the development of a new class of cancer immunotherapy. Herein, we describe the discovery of PVTX-405, a potent, effective, highly selective, and orally efficacious IKZF2 molecular glue degrader. PVTX-405 degrades IKZF2 (DC 50  = 0.7 nM and D max  = 91%) while sparing other CRBN neo-substrates. Degradation of IKZF2 by PVTX-405 increases production of inflammatory cytokine IL-2 and reduces the suppressive activity of Tregs, leading to an increase in Teff cell proliferation. Once-daily oral administration of PVTX-405 as single agent significantly delays the growth of MC38 tumors in a syngeneic tumor model using humanized CRBN mice. PVTX-405 in combination with anti-PD1 or anti-LAG3 significantly increases animal survival compared to anti-PD1 or anti-LAG3 alone. Together, these results demonstrate that PVTX-405 is a promising IKZF2 degrader for clinical development for the treatment of human cancers.


  • Organizational Affiliation
    • Rogel Cancer Center, Department of Internal Medicine, Department of Pharmacology, and, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon
A, C, E, G
111Homo sapiensMutation(s): 0 
Gene Names: CRBNAD-006
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein Helios
B, D, F, H
30Homo sapiensMutation(s): 0 
Gene Names: IKZF2HELIOSZNFN1A2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKS7 (Homo sapiens)
Explore Q9UKS7 
Go to UniProtKB:  Q9UKS7
PHAROS:  Q9UKS7
GTEx:  ENSG00000030419 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKS7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A8N (Subject of Investigation/LOI)
Query on A1A8N

Download Ideal Coordinates CCD File 
I [auth A],
L [auth C],
O [auth E],
R [auth G]
(3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione
C26 H27 N3 O4
HZXUBAMXBADXJI-NRFANRHFSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth A]
K [auth B]
M [auth C]
N [auth D]
P [auth E]
J [auth A],
K [auth B],
M [auth C],
N [auth D],
P [auth E],
Q [auth F],
S [auth G],
T [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.234 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.395α = 90
b = 69.239β = 90.01
c = 79.857γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release