Crystal structure of human BRM in complex with compound 15

Experimental Data Snapshot

  • Resolution: 2.84 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Discovery of Orally Active Inhibitors of Brahma Homolog (BRM)/SMARCA2 ATPase Activity for the Treatment of Brahma Related Gene 1 (BRG1)/SMARCA4-Mutant Cancers.

Papillon, J.P.N.Nakajima, K.Adair, C.D.Hempel, J.Jouk, A.O.Karki, R.G.Mathieu, S.Mobitz, H.Ntaganda, R.Smith, T.Visser, M.Hill, S.E.Hurtado, F.K.Chenail, G.Bhang, H.C.Bric, A.Xiang, K.Bushold, G.Gilbert, T.Vattay, A.Dooley, J.Costa, E.A.Park, I.Li, A.Farley, D.Lounkine, E.Yue, Q.K.Xie, X.Zhu, X.Kulathila, R.King, D.Hu, T.Vulic, K.Cantwell, J.Luu, C.Jagani, Z.

(2018) J Med Chem 61: 10155-10172

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01318
  • Primary Citation of Related Structures:  
    6EG2, 6EG3

  • PubMed Abstract: 

    SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily A member 2 (SMARCA2), also known as Brahma homologue (BRM), is a Snf2-family DNA-dependent ATPase. BRM and its close homologue Brahma-related gene 1 (BRG1), also known as SMARCA4, are mutually exclusive ATPases of the large ATP-dependent SWI/SNF chromatin-remodeling complexes involved in transcriptional regulation of gene expression. No small molecules have been reported that modulate SWI/SNF chromatin-remodeling activity via inhibition of its ATPase activity, an important goal given the well-established dependence of BRG1-deficient cancers on BRM. Here, we describe allosteric dual BRM and BRG1 inhibitors that downregulate BRM-dependent gene expression and show antiproliferative activity in a BRG1-mutant-lung-tumor xenograft model upon oral administration. These compounds represent useful tools for understanding the functions of BRM in BRG1-loss-of-function settings and should enable probing the role of SWI/SNF functions more broadly in different cancer contexts and those of other diseases.

  • Organizational Affiliation

    Novartis Institutes for Biomedical Research , 5300 Chiron Way , Emeryville , California 94608 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,Probable global transcription activator SNF2L2621Escherichia coli O157:H7Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malEZ5632ECs5017SMARCA2BAF190BBRMSNF2ASNF2L2
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 
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP51531P0AEX9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.84 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.47α = 90
b = 136.47β = 90
c = 121.37γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description