5FBN

BTK kinase domain with inhibitor 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/acsmedchemlett.5b00463
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase BTK
C, D
271Homo sapiensMutation(s): 0 
Gene Names: BTK (AGMX1, ATK, BPK)
EC: 2.7.10.2
Find proteins for Q06187 (Homo sapiens)
Go to Gene View: BTK
Go to UniProtKB:  Q06187
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5WE
Query on 5WE

Download SDF File 
Download CCD File 
C, D
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
 Ligand Interaction
5WF
Query on 5WF

Download SDF File 
Download CCD File 
C, D
4-[8-azanyl-3-[(3~{R})-1-(3-methyloxetan-3-yl)carbonylpiperidin-3-yl]imidazo[1,5-a]pyrazin-1-yl]-~{N}-[4-(trifluoromethyl)pyridin-2-yl]benzamide
C29 H28 F3 N7 O3
AHBFBRPGNOVEBK-LJQANCHMSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5WFIC50: 0.17 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.262α = 90.00
b = 71.475β = 90.68
c = 103.056γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references
  • Version 1.2: 2019-04-24
    Type: Data collection, Source and taxonomy