6O0K | pdb_00006o0k

crystal structure of BCL-2 with venetoclax

• PDB DOI: https://doi.org/10.2210/pdb6O0K/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-02-16 Released: 2019-05-22 
• Deposition Author(s): Birkinshaw, R.W., Luo, C.S., Colman, P.M., Czabotar, P.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

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

• PubMed: 31160589 
• DOI: https://doi.org/10.1038/s41467-019-10363-1
• Primary Citation 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.

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Organizational Affiliation: 
• Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. [e-mail].
Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia. [e-mail].
Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia.
Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, 3000, Australia.
Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, 3000, Australia.
Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, 3010, Australia.
Centre for Cancer Research, University of Melbourne, Melbourne, VIC, 3000, Australia.
Victorian Comprehensive Cancer Centre, Melbourne, VIC, 3000, Australia.
Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. [e-mail].
Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.64 kDa 
• Atom Count: 1,512 
• Modeled Residue Count: 141 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator Bcl-2	A	166	Homo sapiens	Mutation(s): 0  Gene Names: BCL2, BCL2L1, BCL2L, BCLX
UniProt & NIH Common Fund Data Resources
Find proteins for P10415 (Homo sapiens) Explore P10415  Go to UniProtKB:  P10415
PHAROS:  P10415 GTEx:  ENSG00000171791
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
PHAROS:  Q07817 GTEx:  ENSG00000171552
UniProt Groups	Q07817P10415

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LBM	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 LQBVNQSMGBZMKD-UHFFFAOYSA-N
2PE	C [auth A]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.725	α = 90
b = 48.506	β = 90
c = 87.316	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): Birkinshaw, R.W., Luo, C.S., Colman, P.M., Czabotar, P.E.

Revision History  

• 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: Data collection, Database references, 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: Structure summary
• Version 2.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary