2YXJ

Crystal structure of Bcl-xL in complex with ABT-737

• PDB DOI: https://doi.org/10.2210/pdb2YXJ/pdb

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


• Deposited: 2007-04-26 Released: 2007-05-22 
• Deposition Author(s): Czabotar, P.E., Lee, E.F., Smith, B.J., Deshayes, K., Zobel, K., Fairlie, W.D., Colman, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.249 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Crystal structure of ABT-737 complexed with Bcl-xL: implications for selectivity of antagonists of the Bcl-2 family

Lee, E.F., Czabotar, P.E., Smith, B.J., Deshayes, K., Zobel, K., Colman, P.M., Fairlie, W.D.

(2007) Cell Death Differ 14: 1711-1713

• PubMed: 17572662 
• DOI: https://doi.org/10.1038/sj.cdd.4402178
• Primary Citation of Related Structures:  
  2YXJ

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.36 kDa 
• Atom Count: 2,608 
• Modelled Residue Count: 279 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator Bcl-X	A, B	181	Homo sapiens	Mutation(s): 0  Gene Names: Bcl-xL
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
PHAROS:  Q07817 GTEx:  ENSG00000171552

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N3C	D [auth A], F [auth B]	4-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1-YL}-N-{[4-({(1R)-3-(DIMETHYLAMINO)-1-[(PHENYLTHIO)METHYL]PROPYL}AMINO)-3-NITROPHENYL]SULFONYL}BENZAMIDE C42 H45 Cl N6 O5 S2 HPLNQCPCUACXLM-PGUFJCEWSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
N3C	PDBBind:  2YXJ	Ki: 0.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.249 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.321	α = 90
b = 75.37	β = 90
c = 87.778	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Czabotar, P.E., Lee, E.F., Smith, B.J., Deshayes, K., Zobel, K., Fairlie, W.D., Colman, P.M.

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-08-16
  Changes: Source and taxonomy
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description