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 

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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: BTK, AGMX1, ATK, BPK
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
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  • 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

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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