6MCY

Crystal structure of mouse Bak


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A small molecule interacts with VDAC2 to block mouse BAK-driven apoptosis.

van Delft, M.F.Chappaz, S.Khakham, Y.Bui, C.T.Debrincat, M.A.Lowes, K.N.Brouwer, J.M.Grohmann, C.Sharp, P.P.Dagley, L.F.Li, L.McArthur, K.Luo, M.X.Chin, H.S.Fairlie, W.D.Lee, E.F.Segal, D.Duflocq, S.Lessene, R.Bernard, S.Peilleron, L.Nguyen, T.Miles, C.Wan, S.S.Lane, R.M.Wardak, A.Lackovic, K.Colman, P.M.Sandow, J.J.Webb, A.I.Czabotar, P.E.Dewson, G.Watson, K.G.Huang, D.C.S.Lessene, G.Kile, B.T.

(2019) Nat Chem Biol 15: 1057-1066

  • DOI: https://doi.org/10.1038/s41589-019-0365-8
  • Primary Citation of Related Structures:  
    6MCY

  • PubMed Abstract: 

    Activating the intrinsic apoptosis pathway with small molecules is now a clinically validated approach to cancer therapy. In contrast, blocking apoptosis to prevent the death of healthy cells in disease settings has not been achieved. Caspases have been favored, but they act too late in apoptosis to provide long-term protection. The critical step in committing a cell to death is activation of BAK or BAX, pro-death BCL-2 proteins mediating mitochondrial damage. Apoptosis cannot proceed in their absence. Here we show that WEHI-9625, a novel tricyclic sulfone small molecule, binds to VDAC2 and promotes its ability to inhibit apoptosis driven by mouse BAK. In contrast to caspase inhibitors, WEHI-9625 blocks apoptosis before mitochondrial damage, preserving cellular function and long-term clonogenic potential. Our findings expand on the key role of VDAC2 in regulating apoptosis and demonstrate that blocking apoptosis at an early stage is both advantageous and pharmacologically tractable.


  • Organizational Affiliation

    Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. vandelft@wehi.edu.au.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bcl-2 homologous antagonist/killer
A, B, C, D
169Mus musculusMutation(s): 1 
Gene Names: Bak1Bak
UniProt
Find proteins for O08734 (Mus musculus)
Explore O08734 
Go to UniProtKB:  O08734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08734
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.951α = 93.14
b = 59.261β = 93.35
c = 79.207γ = 97.63
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1113133

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2019-11-27
    Changes: Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description