6HR2

Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and pVHL:ElonginC:ElonginB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

wwPDB Validation 3D Report Full Report


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:  
    6HR2, 6HAX, 6HAZ, 6HAY

  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription activator BRG1AE120Homo sapiensMutation(s): 0 
Gene Names: SMARCA4BAF190ABRG1SNF2BSNF2L4
EC: 3.6.4
Find proteins for P51532 (Homo sapiens)
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Go to UniProtKB:  P51532
NIH Common Fund Data Resources
PHAROS  P51532
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressorBF149Homo sapiensMutation(s): 0 
Gene Names: VHL
Find proteins for P40337 (Homo sapiens)
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Go to UniProtKB:  P40337
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PHAROS  P40337
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-CCG97Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
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PHAROS  Q15369
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-BDH104Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
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PHAROS  Q15370
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FWZ
Query on FWZ

Download CCD File 
B, F
(2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide
C49 H58 F N9 O6 S
UTZVLJZPTDCKCT-XBPZXCMESA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
B, E
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
F, H
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.332α = 69.43
b = 61.678β = 83.38
c = 81.603γ = 86.42
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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