3ZLR | pdb_00003zlr

Crystal structure of BCL-XL in complex with inhibitor (WEHI-539)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Structure-Guided Design of a Selective Bcl-Xl Inhibitor

Lessene, G.L.Czabotar, P.E.Sleebs, B.E.Zobel, K.Lowes, K.L.Adams, J.M.Baell, J.B.Colman, P.M.Deshayes, K.Fairbrother, W.J.Flygare, J.A.Gibbons, P.Kersten, W.J.A.Kulasegaram, S.Moss, R.M.Parisot, J.P.Smith, B.J.Street, I.P.Yang, H.Huang, D.C.S.Watson, K.G.

(2013) Nat Chem Biol 9: 390-397

  • DOI: https://doi.org/10.1038/nchembio.1246
  • Primary Citation of Related Structures:  
    3ZK6, 3ZLN, 3ZLO, 3ZLR

  • PubMed Abstract: 

    The prosurvival BCL-2 family protein BCL-X(L) is often overexpressed in solid tumors and renders malignant tumor cells resistant to anticancer therapeutics. Enhancing apoptotic responses by inhibiting BCL-X(L) will most likely have widespread utility in cancer treatment and, instead of inhibiting multiple prosurvival BCL-2 family members, a BCL-X(L)-selective inhibitor would be expected to minimize the toxicity to normal tissues. We describe the use of a high-throughput screen to discover a new series of small molecules targeting BCL-X(L) and their structure-guided development by medicinal chemistry. The optimized compound, WEHI-539 (7), has high affinity (subnanomolar) and selectivity for BCL-X(L) and potently kills cells by selectively antagonizing its prosurvival activity. WEHI-539 will be an invaluable tool for distinguishing the roles of BCL-X(L) from those of its prosurvival relatives, both in normal cells and notably in malignant tumor cells, many of which may prove to rely upon BCL-X(L) for their sustained growth.


  • Organizational Affiliation

    Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. glessene@wehi.edu.au


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BCL-2-LIKE PROTEIN 1
A, B
158Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
PHAROS:  Q07817
GTEx:  ENSG00000171552 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07817
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X0B
Query on X0B

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
5-[3-[4-(aminomethyl)phenoxy]propyl]-2-[(8E)-8-(1,3-benzothiazol-2-ylhydrazinylidene)-6,7-dihydro-5H-naphthalen-2-yl]-1,3-thiazole-4-carboxylic acid
C31 H29 N5 O3 S2
JKMWZKPAXZBYEH-JWHWKPFMSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
X0B BindingDB:  3ZLR Ki: 1.1 (nM) from 1 assay(s)
Kd: 1.4 (nM) from 1 assay(s)
IC50: min: 1.1, max: 7.1 (nM) from 3 assay(s)
EC50: 48 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.241α = 90
b = 56.241β = 90
c = 211.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted X0BClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-05-08
    Changes: Database references
  • Version 1.2: 2013-06-05
    Changes: Database references
  • Version 1.3: 2018-06-13
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description