5KUP

Bruton's tyrosine kinase (BTK) with pyridazinone compound 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Battling Btk Mutants With Noncovalent Inhibitors That Overcome Cys481 and Thr474 Mutations.

Johnson, A.R.Kohli, P.B.Katewa, A.Gogol, E.Belmont, L.D.Choy, R.Penuel, E.Burton, L.Eigenbrot, C.Yu, C.Ortwine, D.F.Bowman, K.Franke, Y.Tam, C.Estevez, A.Mortara, K.Wu, J.Li, H.Lin, M.Bergeron, P.Crawford, J.J.Young, W.B.

(2016) ACS Chem Biol 11: 2897-2907

  • DOI: https://doi.org/10.1021/acschembio.6b00480
  • Primary Citation of Related Structures:  
    5KUP

  • PubMed Abstract: 

    The Bruton's tyrosine kinase (Btk) inhibitor ibrutinib has shown impressive clinical efficacy in a range of B-cell malignancies. However, acquired resistance has emerged, and second generation therapies are now being sought. Ibrutinib is a covalent, irreversible inhibitor that modifies Cys481 in the ATP binding site of Btk and renders the enzyme inactive, thereby blocking B-cell receptor signal transduction. Not surprisingly, Cys481 is the most commonly mutated Btk residue in cases of acquired resistance to ibrutinib. Mutations at other sites, including Thr474, a gatekeeper residue, have also been detected. Herein, we describe noncovalent Btk inhibitors that differ from covalent inhibitors like ibrutinib in that they do not interact with Cys481, they potently inhibit the ibrutinib-resistant Btk C481S mutant in vitro and in cells, and they are exquisitely selective for Btk. Noncovalent inhibitors such as GNE-431 also show excellent potency against the C481R, T474I, and T474M mutants. X-ray crystallographic analysis of Btk provides insight into the unique mode of binding of these inhibitors that explains their high selectivity for Btk and their retained activity against mutant forms of Btk. This class of noncovalent Btk inhibitors may provide a treatment option to patients, especially those who have acquired resistance to ibrutinib by mutation of Cys481 or Thr474.


  • Organizational Affiliation

    Biochemical and Cellular Pharmacology, Genentech , 1 DNA Way, South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK271Homo 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6XL
Query on 6XL

Download Ideal Coordinates CCD File 
G [auth A]6-~{tert}-butyl-8-fluoranyl-2-[3-(hydroxymethyl)-4-[1-methyl-6-oxidanylidene-5-(pyrimidin-4-ylamino)pyridin-3-yl]pyridin-2-yl]phthalazin-1-one
C28 H26 F N7 O3
QTEIEFCDHKXATA-UHFFFAOYSA-N
PG0
Query on PG0

Download Ideal Coordinates CCD File 
F [auth A]2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6XL Binding MOAD:  5KUP IC50: 7.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.373α = 90
b = 108.373β = 90
c = 42.453γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
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: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description