6DI9

CRYSTAL STRUCTURE OF BTK IN COMPLEX WITH COVALENT INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GJJ (Subject of Investigation/LOI)
Query on GJJ

Download Ideal Coordinates CCD File 
B [auth A]6-[(3S)-3-(acryloylamino)pyrrolidin-1-yl]-2-{[4-(tert-butylcarbamoyl)phenyl]amino}pyridine-3-carboxamide
C24 H30 N6 O3
AYRMUHGKVWLINC-KRWDZBQOSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GJJ BindingDB:  6DI9 IC50: 7.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.911α = 90
b = 104.61β = 90
c = 38.098γ = 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: 2018-05-23 
  • 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