8QJT

BRM (SMARCA2) Bromodomain in complex with ligand 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

PROTACs Targeting BRM (SMARCA2) Afford Selective In Vivo Degradation over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models.

Berlin, M.Cantley, J.Bookbinder, M.Bortolon, E.Broccatelli, F.Cadelina, G.Chan, E.W.Chen, H.Chen, X.Cheng, Y.Cheung, T.K.Davenport, K.DiNicola, D.Gordon, D.Hamman, B.D.Harbin, A.Haskell, R.He, M.Hole, A.J.Januario, T.Kerry, P.S.Koenig, S.G.Li, L.Merchant, M.Perez-Dorado, I.Pizzano, J.Quinn, C.Rose, C.M.Rousseau, E.Soto, L.Staben, L.R.Sun, H.Tian, Q.Wang, J.Wang, W.Ye, C.S.Ye, X.Zhang, P.Zhou, Y.Yauch, R.Dragovich, P.S.

(2024) J Med Chem 67: 1262-1313

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01781
  • Primary Citation of Related Structures:  
    8QJR, 8QJS, 8QJT

  • PubMed Abstract: 

    The identification of VHL-binding proteolysis targeting chimeras (PROTACs) that potently degrade the BRM protein (also known as SMARCA2) in SW1573 cell-based experiments is described. These molecules exhibit between 10- and 100-fold degradation selectivity for BRM over the closely related paralog protein BRG1 (SMARCA4). They also selectively impair the proliferation of the H1944 "BRG1-mutant" NSCLC cell line, which lacks functional BRG1 protein and is thus highly dependent on BRM for growth, relative to the wild-type Calu6 line. In vivo experiments performed with a subset of compounds identified PROTACs that potently and selectively degraded BRM in the Calu6 and/or the HCC2302 BRG1 mutant NSCLC xenograft models and also afforded antitumor efficacy in the latter system. Subsequent PK/PD analysis established a need to achieve strong BRM degradation (>95%) in order to trigger meaningful antitumor activity in vivo . Intratumor quantitation of mRNA associated with two genes whose transcription was controlled by BRM ( PLAU and KRT80 ) also supported this conclusion.


  • Organizational Affiliation

    Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VLC (Subject of Investigation/LOI)
Query on VLC

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
K [auth C]
2-[6-azanyl-5-[(1R,5S)-8-[2-(2-methoxyethoxy)pyridin-4-yl]-3,8-diazabicyclo[3.2.1]octan-3-yl]pyridazin-3-yl]phenol
C24 H28 N6 O3
VDJLADNPSHUUOZ-HDICACEKSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth B],
J [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.75α = 90
b = 63.75β = 90
c = 88.51γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Database references, Refinement description