Co-structure of BTK kinase domain with L-005085737 inhibitor

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Potent, non-covalent reversible BTK inhibitors with 8-amino-imidazo[1,5-a]pyrazine core featuring 3-position bicyclic ring substitutes.

Liu, J.Guiadeen, D.Krikorian, A.Gao, X.Wang, J.Babu Boga, S.Alhassan, A.B.Yu, W.Selyutin, O.Yu, Y.Anand, R.Xu, J.Kelly, J.Duffy, J.L.Liu, S.Yang, C.Wu, H.Cai, J.Bennett, C.Maloney, K.M.Tyagarajan, S.Gao, Y.D.Fischmann, T.O.Presland, J.Mansueto, M.Xu, Z.Leccese, E.Zhang-Hoover, J.Knemeyer, I.Garlisi, C.G.Stivers, P.Brandish, P.E.Hicks, A.Kim, R.Kozlowski, J.A.

(2020) Bioorg Med Chem Lett 30: 127390-127390

  • DOI: https://doi.org/10.1016/j.bmcl.2020.127390
  • Primary Citation of Related Structures:  
    6X3N, 6X3O, 6X3P

  • PubMed Abstract: 

    Bruton's tyrosine kinase (BTK) is a Tec family kinase with a well-defined role in the B cell receptor (BCR) pathway. It has become an attractive kinase target for selective B cell inhibition, and for the treatment of B cell related diseases. Many BTK inhibitors have been discovered for the treatment of cancer and rheumatoid arthritis, including a series of BTK inhibitors based on 8-amino-imidazo[1,5-a]pyrazine we recently reported. The X-ray crystal structures of BTK with inhibitors were also published, which provided great help for the SAR design. Here we report our SAR work introducing ring constraints for the 3-position piperidine amides on the BTK inhibitors based on 8-amino-imidazo[1,5-a]pyrazine. This modification improved the potency in BTK inhibitions, as well as the PK profile and the off-target selectivity. The dose-dependent efficacy of two BTK inhibitors was observed in the rat collagen induced arthritis (CIA) model.

  • Organizational Affiliation

    Department of Early Development and Discovery Sciences, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA. Electronic address: jian_liu@merck.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK271Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ULV (Subject of Investigation/LOI)
Query on ULV

Download Ideal Coordinates CCD File 
B [auth A]4-{8-amino-3-[(6R,8aS)-3-oxohexahydro-3H-[1,3]oxazolo[3,4-a]pyridin-6-yl]imidazo[1,5-a]pyrazin-1-yl}-N-[4-(trifluoromethyl)pyridin-2-yl]benzamide
C26 H22 F3 N7 O3
Query on 5WE

Download Ideal Coordinates CCD File 
C [auth A]4-[8-azanyl-3-[(2~{S})-1-[4-(dimethylamino)butanoyl]pyrrolidin-2-yl]imidazo[1,5-a]pyrazin-1-yl]-~{N}-(1,3-thiazol-2-yl)benzamide
C26 H30 N8 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
ULV Binding MOAD:  6X3N IC50: 0.08 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.41α = 90
b = 104.83β = 90
c = 38.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references