9D12

Smarca2 Bromodomain in complex with compound 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Discovery of High-Affinity SMARCA2/4 Bromodomain Ligands and Development of Potent and Exceptionally Selective SMARCA2 PROTAC Degraders.

Leng, L.Tu, W.Yang, L.Huang, L.Wang, M.Meagher, J.L.Chinnaswamy, K.Allu, S.R.Rej, R.K.Tosovic, J.Harikrishnan, L.Li, Z.Sui, Z.Stuckey, J.A.Wang, S.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01903

  • PubMed Abstract: 

    In the SWI/SNF chromatin-remodeling complex, the mutually exclusive catalytic ATPase subunits SMARCA2 and SMARCA4 proteins have a synthetic-lethal relationship. Selectively targeting SMARCA2 for degradation is a promising and new therapeutic strategy for human cancers harboring inactivated mutated SMARCA4. In this study, we report the design, synthesis, and biological evaluation of novel SMARCA2/4 ligands and our subsequent design of PROTAC degraders using high-affinity SMARCA ligands and VHL-1 ligands. Our efforts led to the discovery of high-affinity SMARCA2/4 bromodomain ligands and the development of a potent and selective SMARCA2 degrader and a highly potent SMARCA2/4 and PBRM1 degrader.


  • Organizational Affiliation

    Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, 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
124Homo sapiensMutation(s): 0 
Gene Names: SMARCA2BAF190BBRMSNF2ASNF2L2
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51531 (Homo sapiens)
Go to UniProtKB:  P51531
PHAROS:  P51531
GTEx:  ENSG00000080503 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51531-2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A1P (Subject of Investigation/LOI)
Query on A1A1P

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C]
(12'R)-4'-chloro-9'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one
C25 H26 Cl N3 O
MEFDDENEEVLEBY-UHFFFAOYSA-N
ZN
Query on ZN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.897α = 90
b = 67.897β = 90
c = 88.819γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data scaling
HKL-2000data 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: 2025-01-15
    Type: Initial release