7U8F

Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery and characterization of a selective IKZF2 glue degrader for cancer immunotherapy.

Bonazzi, S.d'Hennezel, E.Beckwith, R.E.J.Xu, L.Fazal, A.Magracheva, A.Ramesh, R.Cernijenko, A.Antonakos, B.Bhang, H.C.Caro, R.G.Cobb, J.S.Ornelas, E.Ma, X.Wartchow, C.A.Clifton, M.C.Forseth, R.R.Fortnam, B.H.Lu, H.Csibi, A.Tullai, J.Carbonneau, S.Thomsen, N.M.Larrow, J.Chie-Leon, B.Hainzl, D.Gu, Y.Lu, D.Meyer, M.J.Alexander, D.Kinyamu-Akunda, J.Sabatos-Peyton, C.A.Dales, N.A.Zecri, F.J.Jain, R.K.Shulok, J.Wang, Y.K.Briner, K.Porter, J.A.Tallarico, J.A.Engelman, J.A.Dranoff, G.Bradner, J.E.Visser, M.Solomon, J.M.

(2023) Cell Chem Biol 30: 235-247.e12

  • DOI: https://doi.org/10.1016/j.chembiol.2023.02.005
  • Primary Citation of Related Structures:  
    7U8F, 8DEY

  • PubMed Abstract: 

    Malignant tumors can evade destruction by the immune system by attracting immune-suppressive regulatory T cells (Treg) cells. The IKZF2 (Helios) transcription factor plays a crucial role in maintaining function and stability of Treg cells, and IKZF2 deficiency reduces tumor growth in mice. Here we report the discovery of NVP-DKY709, a selective molecular glue degrader of IKZF2 that spares IKZF1/3. We describe the recruitment-guided medicinal chemistry campaign leading to NVP-DKY709 that redirected the degradation selectivity of cereblon (CRBN) binders from IKZF1 toward IKZF2. Selectivity of NVP-DKY709 for IKZF2 was rationalized by analyzing the DDB1:CRBN:NVP-DKY709:IKZF2(ZF2 or ZF2-3) ternary complex X-ray structures. Exposure to NVP-DKY709 reduced the suppressive activity of human Treg cells and rescued cytokine production in exhausted T-effector cells. In vivo, treatment with NVP-DKY709 delayed tumor growth in mice with a humanized immune system and enhanced immunization responses in cynomolgus monkeys. NVP-DKY709 is being investigated in the clinic as an immune-enhancing agent for cancer immunotherapy.


  • Organizational Affiliation

    Novartis Institutes for Biomedical Research, Cambridge, MA, USA. Electronic address: simone.bonazzi@novartis.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon
A, D
405Homo 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
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
IKZF2
C, F
28Homo sapiensMutation(s): 0 
Gene Names: ZNFN1A2
UniProt
Find proteins for Q53SU9 (Homo sapiens)
Explore Q53SU9 
Go to UniProtKB:  Q53SU9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53SU9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LWK (Subject of Investigation/LOI)
Query on LWK

Download Ideal Coordinates CCD File 
H [auth A],
O [auth D]
(3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione
C25 H27 N3 O3
OMISHRJQMYQPMG-QFIPXVFZSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
Q [auth E]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth B]
J [auth B]
K [auth B]
L [auth B]
P [auth D]
I [auth B],
J [auth B],
K [auth B],
L [auth B],
P [auth D],
R [auth E],
S [auth E],
T [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.892α = 90
b = 180.892β = 90
c = 555.884γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata 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: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2023-03-29
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description