Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66563.23 
• Atom Count: 4496 
• Residue Count: 542 
• 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


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

---

Experimental Data Snapshot

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

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:  
  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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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) Go to Gene View: BTK Go to UniProtKB:  Q06187

Small Molecules

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
5WF	IC50: 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 = 38.262	α = 90.00
b = 71.475	β = 90.68
c = 103.056	γ = 90.00

Software Package:

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

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
  Type: Database references
• Version 1.2: 2019-04-24
  Type: Data collection, Source and taxonomy