5FBO | pdb_00005fbo

BTK-inhibitor co-structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.236 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

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 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
    • Department of Early Development and Discovery Sciences, Merck Research Laboratories , 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States.

Macromolecule Content 

  • Total Structure Weight: 32.7 kDa 
  • Atom Count: 2,259 
  • Modeled Residue Count: 255 
  • Deposited Residue Count: 271 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK271Homo 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
GTEx:  ENSG00000010671 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5WH

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
JUSWPUDQOKINJO-MAUKXSAKSA-N
5WE

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
HUXVNVAKNWKLJM-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.236 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.39α = 90
b = 104.47β = 90
c = 38.08γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
SCALAdata scaling
BUSTERphasing

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
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2026-03-04
    Changes: Refinement description, Structure summary