6O0L

crystal structure of BCL-2 G101V mutation with venetoclax


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1038/s41467-019-10363-1
  • Primary Citation of Related Structures:  

  • 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 ...

    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.,Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. czabotar@wehi.edu.au.,Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. birkinshaw.r@wehi.edu.au.,Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia. birkinshaw.r@wehi.edu.au.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia.,Centre for Cancer Research, University of Melbourne, Melbourne, VIC, 3000, Australia.,Victorian Comprehensive Cancer Centre, Melbourne, VIC, 3000, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia. czabotar@wehi.edu.au.,Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, 3000, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2
A, C
166Homo sapiensMutation(s): 1 
Gene Names: BCL2, BCL2L1 (BCL2L, BCLX)
Find proteins for P10415 (Homo sapiens)
Go to Gene View: BCL2
Go to UniProtKB:  P10415
Find proteins for Q07817 (Homo sapiens)
Go to Gene View: BCL2L1
Go to UniProtKB:  Q07817
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
LBM
Query on LBM

Download SDF File 
Download CCD File 
A, C
4-[4-[[2-(4-chlorophenyl)-4,4-dimethyl-cyclohexen-1-yl]methyl]piperazin-1-yl]-~{N}-[4-(oxan-4-ylmethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]sulfonyl-2-(1~{H}-pyrrolo[2,3-b]pyridin-5-yloxy)benzamide
2-((1H-pyrrolo[2,3-b]pyridin-5-yl)oxy)-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-(((tetrahydro-2H-pyran-4-yl)methyl)amino)phenyl)sulfonyl)benzamide
C45 H51 Cl N7 O7 S
FPPGLAXBEWPSEC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 33.147α = 90.00
b = 82.005β = 90.08
c = 47.508γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-19
    Type: Data collection, Database references
  • Version 1.2: 2019-07-10
    Type: Data collection, Database references, Source and taxonomy, Structure summary