9GIT

BFL1 covalently bound to inhibitor compound 43


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 
    0.212 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Structure-Based Discovery of a Series of Covalent, Orally Bioavailable, and Selective BFL1 Inhibitors.

Palisse, A.Cheung, T.Blokhuis, A.Cogswell, T.Martins, B.S.Riemens, R.Schellekens, R.Battocchio, G.Jansen, C.Cottee, M.A.Ornell, K.Sacchetto, C.Leon, L.van Hoek-Emmelot, M.Bostock, M.Brauer, B.L.Beaumont, K.Lucas, S.C.C.Ahmed, S.Blackwell, J.H.Borjesson, U.Gohlke, A.Gramatikov, I.M.T.Hargreaves, D.van Hoeven, V.Kantae, V.Kupcova, L.Milbradt, A.G.Seneviratne, U.Su, N.Vales, J.Wang, H.White, M.J.Kinzel, O.

(2024) J Med Chem 67: 22055-22079

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01995
  • Primary Citation of Related Structures:  
    9GIP, 9GIQ, 9GIR, 9GIS, 9GIT

  • PubMed Abstract: 

    BFL1, a member of the antiapoptotic BCL2 family, has been relatively understudied compared to its counterparts despite evidence of its overexpression in various hematological malignancies. Across two articles, we describe the development of BFL1 in vivo tools. The first article describes the hit identification from a covalent fragment library and the subsequent evolution from the hit to compound 6 . 22 This work reports the structure-based optimization of compound 6 into a series of BFL1 inhibitors selective over the other BCL2 family members, with low nanomolar cellular activity when combined with AZD5991, exemplified by compound 20 . Compound 20 demonstrated a cell death phenotype in SUDHL1 and OCILY10 cell lines and in the in vivo study, BFL1 stabilization and cleaved caspase 3 activation were observed in a dose-dependent manner. In addition, the enzymatic turnover studies with the BFL1 protein showed that compound 20 stabilized the protein, extending the half-life to 10.8 h.


  • Organizational Affiliation

    Medicinal Chemistry, Oncology, R&D, Acerta Pharma B.V., A member of the AstraZeneca Group, Oss 5349 AB, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bcl-2-related protein A1152Homo sapiensMutation(s): 0 
Gene Names: BCL2A1BCL2L5BFL1GRSHBPA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16548 (Homo sapiens)
Explore Q16548 
Go to UniProtKB:  Q16548
PHAROS:  Q16548
GTEx:  ENSG00000140379 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16548
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ILW (Subject of Investigation/LOI)
Query on A1ILW

Download Ideal Coordinates CCD File 
B [auth A](3~{S})-3-[[4-[(1~{R},3~{R})-3-[[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]carbamoylamino]cyclopentyl]oxy-3-fluoranyl-phenyl]-propanoyl-amino]-3-(4-chlorophenyl)propanamide
C28 H34 Cl F N4 O6 S
NLVAPRIBNJZHAA-QVHJCDIPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free:  0.212 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.329α = 90
b = 42.854β = 101.02
c = 43.138γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
Cootmodel building

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 A1ILWClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2024-12-18 
  • Deposition Author(s): Cottee, M.A.

Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-01-08
    Changes: Database references