5FBO

BTK-inhibitor co-structure

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

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:  
    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 s ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK A271Homo sapiensMutation(s): 0 
Gene Names: BTK, AGMX1, ATK, BPK
EC: 2.7.10.2
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
NIH Common Fund Data Resources
PHAROS:  Q06187
GTEx:  ENSG00000010671
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5WH
Query on 5WH
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
5WE
Query on 5WE
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5WHIC50:  10   nM  BindingDB
5WHIC50:  0.30000001192092896   nM  BindingDB
5WHIC50:  4   nM  BindingDB
5WHIC50:  0.3100000023841858   nM  Binding MOAD
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
BUSTERrefinement
XDSdata reduction
AutoPROCdata scaling
SCALAdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2015-12-14 
  • Released Date: 2016-03-23 
    • Deposition Author(s): Fischmann, T.O.

Revision History 

  • 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