9E30

Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

Starting Model: experimental
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Literature

Discovery of Potent, Highly Selective, and Efficacious SMARCA2 Degraders.

Li, Z.Harikrishnan, L.S.Xu, G.Samanta, D.Clemente, J.C.Leng, L.Tu, W.Yang, L.Huang, L.Wang, M.Wang, S.Deng, Q.Behshad, E.Nagilla, R.Orth, P.Rice, C.Strickland, C.Mohammad, H.P.Priestley, E.S.Sui, Z.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01878
  • Primary Citation of Related Structures:  
    9E1K, 9E30, 9E31

  • PubMed Abstract: 

    We describe the identification of selective SMARCA2, VHL-based heterobifunctional degraders. Structurally novel indolo[1,2- a ]quinazolin-5(7 H )-one SMARCA bromodomain binders were optimized and then converted to SMARCA2 degraders by linking them to well-defined VHL ligands. Our exploration led to the discovery of potent and selective degraders of SMARCA2 over the SMARCA4 paralog, leading to potent and selective growth inhibition of SMARCA4 mutant versus wild type cell lines. We further highlight the optimization of the pharmacokinetic profile of a subset of compounds leading to potent and selective degradation of SMARCA2 in the xenograft model. These compounds provide valuable tools with desirable properties for continued exploration of the biology defining the susceptibility of SMARCA4 mutant cancers to selective loss of SMARCA2.


  • Organizational Affiliation

    SK Life Science Labs, 2500 Renaissance Blvd, King of Prussia, Pennsylvania 19406, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Short of Probable global transcription activator SNF2L2
A, B, C
123Homo sapiensMutation(s): 0 
Gene Names: SMARCA2BAF190BBRMSNF2ASNF2L2
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51531 (Homo sapiens)
Explore P51531 
Go to UniProtKB:  P51531
PHAROS:  P51531
GTEx:  ENSG00000080503 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51531
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A1O (Subject of Investigation/LOI)
Query on A1A1O

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]
(12'S)-4'-chloro-10'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one
C25 H26 Cl N3 O
JKAGLEAKJQWJPR-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
L [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.84α = 90
b = 61.84β = 90
c = 89.16γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing

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: 2024-12-18
    Type: Initial release