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



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 ...

    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 BTK A271Homo sapiensMutation(s): 0 
Gene Names: BTK, AGMX1, ATK, BPK
EC: 2.7.10.2
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
NIH Common Fund Data Resources
PHAROS:  Q06187
GTEx:  ENSG00000010671
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GJJ
Query on GJJ
Download Ideal Coordinates CCD File 
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 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
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

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2018-05-23 
  • Released Date: 2018-09-05 
    • Deposition Author(s): GARDBERG, A.

Revision History 

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