crystal structure of BCL-2 F104L mutation with venetoclax

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

Starting Model: experimental
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Structures of BCL-2 in complex with venetoclax reveal the molecular basis of resistance mutations.

Birkinshaw, R.W.Gong, J.N.Luo, C.S.Lio, D.White, C.A.Anderson, M.A.Blombery, P.Lessene, G.Majewski, I.J.Thijssen, R.Roberts, A.W.Huang, D.C.S.Colman, P.M.Czabotar, P.E.

(2019) Nat Commun 10: 2385-2385

  • DOI: https://doi.org/10.1038/s41467-019-10363-1
  • Primary Citation of Related Structures:  
    6O0K, 6O0L, 6O0M, 6O0O, 6O0P

  • PubMed Abstract: 

    Venetoclax is a first-in-class cancer therapy that interacts with the cellular apoptotic machinery promoting apoptosis. Treatment of patients suffering chronic lymphocytic leukaemia with this BCL-2 antagonist has revealed emergence of a drug-selected BCL-2 mutation (G101V) in some patients failing therapy. To understand the molecular basis of this acquired resistance we describe the crystal structures of venetoclax bound to both BCL-2 and the G101V mutant. The pose of venetoclax in its binding site on BCL-2 reveals small but unexpected differences as compared to published structures of complexes with venetoclax analogues. The G101V mutant complex structure and mutant binding assays reveal that resistance is acquired by a knock-on effect of V101 on an adjacent residue, E152, with venetoclax binding restored by a E152A mutation. This provides a framework for considering analogues of venetoclax that might be effective in combating this mutation.

  • Organizational Affiliation

    Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. birkinshaw.r@wehi.edu.au.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2166Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
GTEx:  ENSG00000171552 
Find proteins for P10415 (Homo sapiens)
Explore P10415 
Go to UniProtKB:  P10415
GTEx:  ENSG00000171791 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ07817P10415
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LBM (Subject of Investigation/LOI)
Query on LBM

Download Ideal Coordinates CCD File 
B [auth A]4-{4-[(4'-chloro-5,5-dimethyl[3,4,5,6-tetrahydro[1,1'-biphenyl]]-2-yl)methyl]piperazin-1-yl}-N-[(3-nitro-4-{[(oxan-4-yl )methyl]amino}phenyl)sulfonyl]-2-[(1H-pyrrolo[2,3-b]pyridin-5-yl)oxy]benzamide
C45 H50 Cl N7 O7 S
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
C4 H10 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.69α = 90
b = 48.27β = 90
c = 87.8γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-10
    Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.0: 2019-11-20
    Changes: Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-12-11
    Changes: Advisory, Derived calculations, Structure summary
  • Version 2.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary