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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/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. 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. Electronic address: hui.qiu@emdserono.com.


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 1 Unique
IDChains Name / 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
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

  • 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
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references