6DI3

CRYSTAL STRUCTURE OF BTK IN COMPLEX WITH FRAGMENT LIGAND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.200 

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This is version 1.0 of the entry. See complete history


Literature

Discovery of potent, highly selective covalent irreversible BTK inhibitors from a fragment hit.

Qiu, H.Liu-Bujalski, L.Caldwell, R.D.Follis, A.V.Gardberg, A.Goutopoulos, A.Grenningloh, R.Head, J.Johnson, T.Jones, R.Mochalkin, I.Morandi, F.Neagu, C.Sherer, B.

(2018) Bioorg Med Chem Lett 28: 2939-2944

  • DOI: 10.1016/j.bmcl.2018.07.008
  • Primary Citation of Related Structures:  
    6DI3, 6DI5, 6DI9

  • PubMed Abstract: 
  • Bruton's Tyrosine Kinase (BTK) is a member of the TEC kinase family that is expressed in cells of hematopoietic lineage (e.g., in B cells, macrophages, monocytes, and mast cells). Small molecule covalent irreversible BTK inhibitor targeting Cys481 within the ATP-binding pocket, for example ibrutinib, has been applied in the treatment of B-cell malignancies ...

    Bruton's Tyrosine Kinase (BTK) is a member of the TEC kinase family that is expressed in cells of hematopoietic lineage (e.g., in B cells, macrophages, monocytes, and mast cells). Small molecule covalent irreversible BTK inhibitor targeting Cys481 within the ATP-binding pocket, for example ibrutinib, has been applied in the treatment of B-cell malignancies. Starting from a fragment hit, we discovered a novel series of potent covalent irreversible BTK inhibitors that occupy selectivity pocket of the active site of the BTK kinase domain. Guided by X-ray structures and a fragment-based drug design (FBDD) approach, we generated molecules showing comparable cellular potency to ibrutinib and higher kinome selectivity against undesirable off-targets like EGFR.


    Organizational Affiliation

    EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica 01821, MA, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTKA271Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GJA (Subject of Investigation/LOI)
Query on GJA

Download Ideal Coordinates CCD File 
B [auth A]6-[(3S)-3-(acryloylamino)pyrrolidin-1-yl]-2-(4-phenoxyphenoxy)pyridine-3-carboxamide
C25 H24 N4 O4
VMINNJIVIPLCSD-KRWDZBQOSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GJA BindingDB:  6DI3 IC50: 25 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.1α = 90
b = 104.96β = 90
c = 38.08γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-05-22 
  • Released Date: 2018-09-05 
  • Deposition Author(s): GARDBERG, A.

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release