6RNU

BCL-XL in a complex with a covalent small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery and optimization of covalent Bcl-xL antagonists.

Mukherjee, H.Su, N.Belmonte, M.A.Hargreaves, D.Patel, J.Tentarelli, S.Aquila, B.Grimster, N.P.

(2019) Bioorg Med Chem Lett 29: 126682-126682

  • DOI: 10.1016/j.bmcl.2019.126682
  • Primary Citation of Related Structures:  
    6RNU

  • PubMed Abstract: 
  • Over the last ten years, targeted covalent inhibition has become a key discipline within medicinal chemistry research, most notably in the development of oncology therapeutics. One area where this approach is underrepresented, however, is in targeting protein-protein interactions ...

    Over the last ten years, targeted covalent inhibition has become a key discipline within medicinal chemistry research, most notably in the development of oncology therapeutics. One area where this approach is underrepresented, however, is in targeting protein-protein interactions. This is primarily because these hydrophobic interfaces lack appropriately located cysteine residues to allow for standard conjugate addition chemistry. Herein, we report our development of the first covalent inhibitors of the antiapoptotic protein B-cell lymphoma extra-large (Bcl-xL), utilizing a sulfonyl fluoride (SF) warhead to selectively covalently modify tyrosine 101 of the BH3 domain-binding groove. These compounds display time-dependent inhibition in a biochemical assay and are cellularly active (U266B1). In addition, compound 7 was further elaborated to generate a chemical-biology probe molecule, which may find utility in understanding the intricacies of Bcl-xL biology.


    Organizational Affiliation

    Oncology R&D, AstraZeneca, Waltham, USA. Electronic address: neil.grimster@astrazeneca.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bcl-2-like protein 1A, B177Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KBH (Subject of Investigation/LOI)
Query on KBH

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]4-(4-fluorophenyl)-3-fluorosulfonyl-benzoic acid
C13 H8 F2 O4 S
HNGNJNXHCQAHBJ-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download Ideal Coordinates CCD File 
E [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.59α = 90
b = 96.59β = 90
c = 86.4γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2019-05-09 
  • Released Date: 2019-10-02 
  • Deposition Author(s): Hargreaves, D.

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Database references