BTK-inhibitor co-structure

Experimental Data Snapshot

  • Resolution: 1.89 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

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This is version 1.2 of the entry. See complete history


Discovery of 8-Amino-imidazo[1,5-a]pyrazines as Reversible BTK Inhibitors for the Treatment of Rheumatoid Arthritis.

Liu, J.Guiadeen, D.Krikorian, A.Gao, X.Wang, J.Boga, S.B.Alhassan, A.B.Yu, Y.Vaccaro, H.Liu, S.Yang, C.Wu, H.Cooper, A.de Man, J.Kaptein, A.Maloney, K.Hornak, V.Gao, Y.D.Fischmann, T.O.Raaijmakers, H.Vu-Pham, D.Presland, J.Mansueto, M.Xu, Z.Leccese, E.Zhang-Hoover, J.Knemeyer, I.Garlisi, C.G.Bays, N.Stivers, P.Brandish, P.E.Hicks, A.Kim, R.Kozlowski, J.A.

(2016) ACS Med Chem Lett 7: 198-203

  • DOI: https://doi.org/10.1021/acsmedchemlett.5b00463
  • Primary Citation of Related Structures:  
    5FBN, 5FBO

  • 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. We report a series of compounds based on 8-amino-imidazo[1,5-a]pyrazine that are potent reversible BTK inhibitors with excellent kinase selectivity. Selectivity is achieved through specific interactions of the ligand with the kinase hinge and driven by aminopyridine hydrogen bondings with Ser538 and Asp539, and by hydrophobic interaction of trifluoropyridine in the back pocket. These interactions are evident in the X-ray crystal structure of the lead compounds 1 and 3 in the complex with the BTK enzyme. Our lead compounds show desirable PK profiles and efficacy in the preclinical rat collagen induced arthritis model.

  • Organizational Affiliation

    WuXi PharmaTech Co. Ltd , 288 FuTe Zhong Road, No. 1 Building, WaiGaoQiao Free Trade Zone, Shanghai 200131, P. R. China.

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
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
Query on 5WH

Download Ideal Coordinates CCD File 
B [auth A]4-[8-azanyl-3-[(3~{R},6~{S})-1-cyclopropylcarbonyl-6-methyl-piperidin-3-yl]imidazo[1,5-a]pyrazin-1-yl]-3-fluoranyl-~{N}-[4-(trifluoromethyl)pyridin-2-yl]benzamide
C29 H27 F4 N7 O2
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
5WH Binding MOAD:  5FBO IC50: 0.31 (nM) from 1 assay(s)
BindingDB:  5FBO IC50: min: 0.3, max: 94 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.39α = 90
b = 104.47β = 90
c = 38.08γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
AutoPROCdata scaling
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references