Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.56 kDa 
• Atom Count: 5015 
• Residue Count: 511 
• Unique protein chains: 1

5FBN

BTK kinase domain with inhibitor 1

• DOI: 10.2210/pdb5FBN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-12-14 Released: 2016-02-03 
• Deposition Author(s): Raaijmakers, H.C.A., Vu-Pham, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

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

• PubMed: 26985298 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	C, D	271	Homo sapiens	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5WF	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
5WE	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
EDO	D	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C, D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
5WF	IC50:  0.30000001192092896   nM  BindingDB
5WF	EC50:  10   nM  BindingDB
5WF	IC50:  0.17000000178813934   nM  Binding MOAD
5WF	IC50:  8   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.262	α = 90
b = 71.475	β = 90.68
c = 103.056	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-12-14 
• Released Date: 2016-02-03 
Deposition Author(s): Raaijmakers, H.C.A., Vu-Pham, D.

Revision History 

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