7LPS

Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2)

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2021-02-12 Released: 2021-06-02 
  • Deposition Author(s): Nowak, R.P., Fischer, E.S.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Damon Runyon Cancer Research Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.78 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.289 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Acute pharmacological degradation of Helios destabilizes regulatory T cells.

Wang, E.S.Verano, A.L.Nowak, R.P.Yuan, J.C.Donovan, K.A.Eleuteri, N.A.Yue, H.Ngo, K.H.Lizotte, P.H.Gokhale, P.C.Gray, N.S.Fischer, E.S.

(2021) Nat Chem Biol 17: 711-717

  • DOI: https://doi.org/10.1038/s41589-021-00802-w
  • Primary Citation of Related Structures:  
    7LPS

  • PubMed Abstract: 

    The zinc-finger transcription factor Helios is critical for maintaining the identity, anergic phenotype and suppressive activity of regulatory T (T reg ) cells. While it is an attractive target to enhance the efficacy of currently approved immunotherapies, no existing approaches can directly modulate Helios activity or abundance. Here, we report the structure-guided development of small molecules that recruit the E3 ubiquitin ligase substrate receptor cereblon to Helios, thereby promoting its degradation. Pharmacological Helios degradation destabilized the anergic phenotype and reduced the suppressive activity of T reg cells, establishing a route towards Helios-targeting therapeutics. More generally, this study provides a framework for the development of small-molecule degraders for previously unligandable targets by reprogramming E3 ligase substrate specificity.


  • Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1
A, D, G, J
1,140Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon
B, E, H, K
390Homo 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein Helios
C, F, I, L
29Homo 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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RN9 (Subject of Investigation/LOI)
Query on RN9

Download Ideal Coordinates CCD File 
N [auth B],
Q [auth E],
T [auth H],
W [auth K]
3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide
C25 H23 Cl N4 O5
YDYSAFPHVGVORZ-FQEVSTJZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
M [auth B]
O [auth C]
P [auth E]
R [auth F]
S [auth H]
M [auth B],
O [auth C],
P [auth E],
R [auth F],
S [auth H],
U [auth I],
V [auth K],
X [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.78 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.289 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.8α = 90
b = 117.292β = 97.3
c = 196.713γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA214608
Damon Runyon Cancer Research FoundationUnited StatesDRR-50-18

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description