7JGV

CRYSTAL STRUCTURE OF BCL-XL IN COMPLEX WITH COMPOUND 1620116, CRYSTAL FORM 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Optimization of Benzothiazole and Thiazole Hydrazones as Inhibitors of Schistosome BCL-2.

Nguyen, W.Lee, E.F.Evangelista, M.Lee, M.Harris, T.J.Colman, P.M.Smith, N.A.Williams, L.B.Jarman, K.E.Lowes, K.N.Haeberli, C.Keiser, J.Smith, B.J.Fairlie, W.D.Sleebs, B.E.

(2021) ACS Infect Dis 7: 1143-1163

  • DOI: https://doi.org/10.1021/acsinfecdis.0c00700
  • Primary Citation of Related Structures:  
    7JGV, 7JGW, 7JMT

  • PubMed Abstract: 

    Limited therapeutic options are available for the treatment of human schistosomiasis caused by the parasitic Schistosoma flatworm. The B cell lymphoma-2 (BCL-2)-regulated apoptotic cell death pathway in schistosomes was recently characterized and shown to share similarities with the intrinsic apoptosis pathway in humans. Here, we exploit structural differences in the human and schistosome BCL-2 (sBCL-2) pro-survival proteins toward a novel treatment strategy for schistosomiasis. The benzothiazole hydrazone scaffold previously employed to target human BCL-XL was repurposed as a starting point to target sBCL-2. We utilized X-ray structural data to inform optimization and then applied a scaffold-hop strategy to identify the 5-carboxamide thiazole hydrazone scaffold ( 43 ) with potent sBCL-2 activity (IC 50 30 nM). Human BCL-XL potency (IC 50 13 nM) was inadvertently preserved during the optimization process. The lead analogues from this study exhibit on-target activity in model fibroblast cell lines dependent on either sBCL-2 or human BCL-XL for survival. Further optimization of the thiazole hydrazone class is required to exhibit activity in schistosomes and enhance the potential of this strategy for treating schistosomiasis.


  • Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.


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 
Gene Names: BCL2L1BCL2LBCLX
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V9S (Subject of Investigation/LOI)
Query on V9S

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-[(8E)-8-{2-[4-(benzylcarbamoyl)-1,3-thiazol-2-yl]hydrazinylidene}-5,6,7,8-tetrahydronaphthalen-2-yl]-3-(2-phenylethoxy)pyridine-2-carboxylic acid
C35 H31 N5 O4 S
LPGFMHLHQPZQLK-YWIBTEMISA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.324α = 90
b = 56.256β = 90
c = 117.756γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaDevelopment Grant 1135421
National Health and Medical Research Council (NHMRC, Australia)AustraliaProject Grant 1143974
National Health and Medical Research Council (NHMRC, Australia)AustraliaProject Grant 1002227

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description