8RPO

BFL1 in complex with a reversible covalent ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

Starting Model: experimental
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Literature

Identification and Evaluation of Reversible Covalent Binders to Cys55 of Bfl-1 from a DNA-Encoded Chemical Library Screen.

Lucas, S.C.C.Blackwell, J.H.Borjesson, U.Hargreaves, D.Milbradt, A.G.Ahmed, S.Bostock, M.J.Guerot, C.Gohlke, A.Kinzel, O.Lamb, M.L.Selmi, N.Stubbs, C.J.Su, N.Su, Q.Luo, H.Xiong, T.Zuo, X.Bazzaz, S.Bienstock, C.Centrella, P.A.Denton, K.E.Gikunju, D.Guie, M.A.Guilinger, J.P.Hupp, C.Keefe, A.D.Satoh, T.Zhang, Y.Rivers, E.L.

(2024) ACS Med Chem Lett 15: 791-797

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00113
  • Primary Citation of Related Structures:  
    8RPO

  • PubMed Abstract: 

    Bfl-1 is overexpressed in both hematological and solid tumors; therefore, inhibitors of Bfl-1 are highly desirable. A DNA-encoded chemical library (DEL) screen against Bfl-1 identified the first known reversible covalent small-molecule ligand for Bfl-1. The binding was validated through biophysical and biochemical techniques, which confirmed the reversible covalent mechanism of action and pointed to binding through Cys55. This represented the first identification of a cyano-acrylamide reversible covalent compound from a DEL screen and highlights further opportunities for covalent drug discovery through DEL screening. A 10-fold improvement in potency was achieved through a systematic SAR exploration of the hit. The more potent analogue compound 13 was successfully cocrystallized in Bfl-1, revealing the binding mode and providing further evidence of a covalent interaction with Cys55.


  • Organizational Affiliation

    Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.


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
GTEx:  ENSG00000140379 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16548
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H2C (Subject of Investigation/LOI)
Query on A1H2C

Download Ideal Coordinates CCD File 
B [auth A](~{E})-2-cyano-3-(2-dimethylphosphorylphenyl)-~{N}-[[1-[4-(trifluoromethyl)phenyl]cyclopropyl]methyl]prop-2-enamide
C23 H22 F3 N2 O2 P
OMAUAIOHGJMUIU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.748α = 90
b = 69.748β = 90
c = 72.827γ = 120
Software Package:
Software NamePurpose
autoPROCdata reduction
STARANISOdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release