9QAD | pdb_00009qad

Crystal structure of the SMARCA2 bromodomain bound to a tricyclic pyrimidoindolone inhibitor (compound 17)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.245 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Discovery of Pyrimidoindolones as Novel Family VIII Bromodomain Binders.

Boerth, J.A.Schimpl, M.Lucas, S.C.C.Zhang, J.Code, E.L.Embrey, K.J.Rawlins, P.B.Wang, H.Storer, R.I.Di Fruscia, P.Nelson, J.E.Milbradt, A.G.Borjesson, U.Gohlke, A.Korboukh, V.Gopalsamy, A.

(2025) ACS Med Chem Lett 16: 1073-1079

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00120
  • Primary Citation of Related Structures:  
    9QAC, 9QAD

  • PubMed Abstract: 

    Suppression of oncogenic gene expression is an effective strategy for the treatment of cancer. The SWI/SNF (SWItch/Sucrose Non-Fermentable) complex plays an important role in regulating gene activation or repression, and its dysregulation has been linked to aberrant transcription activity in many types of cancer. Targeting the subunits of this complex, such as SMARCA2, SMARCA4, and PBRM1, which are part of the bromodomain family VIII, has significant therapeutic potential. Herein we report the discovery of pyrimidoindolones as a novel series of bromodomain family VIII binders identified through an NMR-based fragment screen. These binders have been optimized to achieve sub-μM affinity for the family VIII proteins SMARCA2, SMARCA4, and PRBM1, with promising physicochemical properties.


  • Organizational Affiliation
    • Medicinal Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.245 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.023α = 90
b = 64.023β = 90
c = 88.985γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
Aimlessdata scaling
XDSdata reduction
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-05-14 
  • Deposition Author(s): Schimpl, M.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references
  • Version 1.2: 2025-06-04
    Changes: Derived calculations
  • Version 1.3: 2025-07-02
    Changes: Database references