6NZM

Brutons tyrosine kinase in complex with compound 50.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Optimization of novel reversible Bruton's tyrosine kinase inhibitors identified using Tethering-fragment-based screens.

Hopkins, B.T.Bame, E.Bell, N.Bohnert, T.Bowden-Verhoek, J.K.Bui, M.Cancilla, M.T.Conlon, P.Cullen, P.Erlanson, D.A.Fan, J.Fuchs-Knotts, T.Hansen, S.Heumann, S.Jenkins, T.J.Marcotte, D.McDowell, B.Mertsching, E.Negrou, E.Otipoby, K.L.Poreci, U.Romanowski, M.J.Scott, D.Silvian, L.Yang, W.Zhong, M.

(2019) Bioorg Med Chem 27: 2905-2913

  • DOI: https://doi.org/10.1016/j.bmc.2019.05.021
  • Primary Citation of Related Structures:  
    6NZM

  • PubMed Abstract: 

    Since the approval of ibrutinib for the treatment of B-cell malignancies in 2012, numerous clinical trials have been reported using covalent inhibitors to target Bruton's tyrosine kinase (BTK) for oncology indications. However, a formidable challenge for the pharmaceutical industry has been the identification of reversible, selective, potent molecules for inhibition of BTK. Herein, we report application of Tethering-fragment-based screens to identify low molecular weight fragments which were further optimized to improve on-target potency and ADME properties leading to the discovery of reversible, selective, potent BTK inhibitors suitable for pre-clinical proof-of-concept studies.


  • Organizational Affiliation

    Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States. Electronic address: Brian.Hopkins@biogen.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTKA,
B [auth D]
280Homo sapiensMutation(s): 0 
Gene Names: BTKAGMX1ATKBPK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
PHAROS:  Q06187
GTEx:  ENSG00000010671 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L9S
Query on L9S

Download Ideal Coordinates CCD File 
C [auth A],
E [auth D]
N-[2-fluoro-6-(pyrrolidin-1-yl)phenyl]-N'-{3-[(2R)-1-(2-hydroxyethyl)-4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazin-2-yl]phenyl}urea
C29 H33 F N8 O2
ZJSNZHATZAWKIQ-VWLOTQADSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
F [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
L9S Binding MOAD:  6NZM IC50: 1 (nM) from 1 assay(s)
BindingDB:  6NZM IC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.297α = 90
b = 71.709β = 89.95
c = 104.41γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references