6HAZ

Crystal structure of the bromodomain of human SMARCA2 in complex with SMARCA-BD ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design.

Farnaby, W.Koegl, M.Roy, M.J.Whitworth, C.Diers, E.Trainor, N.Zollman, D.Steurer, S.Karolyi-Oezguer, J.Riedmueller, C.Gmaschitz, T.Wachter, J.Dank, C.Galant, M.Sharps, B.Rumpel, K.Traxler, E.Gerstberger, T.Schnitzer, R.Petermann, O.Greb, P.Weinstabl, H.Bader, G.Zoephel, A.Weiss-Puxbaum, A.Ehrenhofer-Wolfer, K.Wohrle, S.Boehmelt, G.Rinnenthal, J.Arnhof, H.Wiechens, N.Wu, M.Y.Owen-Hughes, T.Ettmayer, P.Pearson, M.McConnell, D.B.Ciulli, A.

(2019) Nat Chem Biol 15: 672-680

  • DOI: 10.1038/s41589-019-0294-6
  • Primary Citation of Related Structures:  
    6HAX, 6HAY, 6HAZ, 6HR2

  • PubMed Abstract: 
  • Targeting subunits of BAF/PBAF chromatin remodeling complexes has been proposed as an approach to exploit cancer vulnerabilities. Here, we develop proteolysis targeting chimera (PROTAC) degraders of the BAF ATPase subunits SMARCA2 and SMARCA4 using a bromodomain ligand and recruitment of the E3 ubiquitin ligase VHL ...

    Targeting subunits of BAF/PBAF chromatin remodeling complexes has been proposed as an approach to exploit cancer vulnerabilities. Here, we develop proteolysis targeting chimera (PROTAC) degraders of the BAF ATPase subunits SMARCA2 and SMARCA4 using a bromodomain ligand and recruitment of the E3 ubiquitin ligase VHL. High-resolution ternary complex crystal structures and biophysical investigation guided rational and efficient optimization toward ACBI1, a potent and cooperative degrader of SMARCA2, SMARCA4 and PBRM1. ACBI1 induced anti-proliferative effects and cell death caused by SMARCA2 depletion in SMARCA4 mutant cancer cells, and in acute myeloid leukemia cells dependent on SMARCA4 ATPase activity. These findings exemplify a successful biophysics- and structure-based PROTAC design approach to degrade high profile drug targets, and pave the way toward new therapeutics for the treatment of tumors sensitive to the loss of BAF complex ATPases.


    Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK. a.ciulli@dundee.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable global transcription activator SNF2L2A, B123Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51531
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FX5 (Subject of Investigation/LOI)
Query on FX5

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
2-(6-azanyl-5-piperazin-4-ium-1-yl-pyridazin-3-yl)phenol
C14 H18 N5 O
SZKHGLTYXIDOFH-UHFFFAOYSA-O
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.549α = 90
b = 42.549β = 90
c = 164.23γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-03
    Changes: Data collection, Database references