6HAY

Crystal structure of PROTAC 1 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 

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:  

  • 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

    Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.,Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK. a.ciulli@dundee.ac.uk.,Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria. darryl.mcconnell@boehringer-ingelheim.com.,Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.,Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable global transcription activator SNF2L2
A, E
123Homo sapiensMutation(s): 0 
Gene Names: SMARCA2 (BAF190B, BRM, SNF2A, SNF2L2)
EC: 3.6.4.-
Find proteins for P51531 (Homo sapiens)
Go to Gene View: SMARCA2
Go to UniProtKB:  P51531
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
von Hippel-Lindau disease tumor suppressor
B, F
162Homo sapiensMutation(s): 0 
Gene Names: VHL
Find proteins for P40337 (Homo sapiens)
Go to Gene View: VHL
Go to UniProtKB:  P40337
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Elongin-C
C, G
97Homo sapiensMutation(s): 0 
Gene Names: ELOC (TCEB1)
Find proteins for Q15369 (Homo sapiens)
Go to Gene View: ELOC
Go to UniProtKB:  Q15369
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Elongin-B
D, H
104Homo sapiensMutation(s): 0 
Gene Names: ELOB (TCEB2)
Find proteins for Q15370 (Homo sapiens)
Go to Gene View: ELOB
Go to UniProtKB:  Q15370
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
F
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
B, C, D, F, G, H
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FX8
Query on FX8

Download SDF File 
Download CCD File 
B, F
(2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]ethoxy]ethoxy]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
C46 H60 F N9 O8 S
QCULBRPVCWJUKY-OUMVKTTMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 79.725α = 90.00
b = 117.260β = 90.00
c = 121.557γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilERC-2012-StG-311460 DrugE3CRLs

Revision History 

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