9ME3 | pdb_00009me3

Bruton's tyrosine kinase with mutations in the activation loop in complex with compound P301390

• PDB DOI: https://doi.org/10.2210/pdb9ME3/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-12-06 Released: 2025-08-13 
• Deposition Author(s): Lin, D.Y., Andreotti, A.H., Tonge, P.J., Bravo, E., Li, X.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.288 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Modulating the Binding Kinetics of Bruton's Tyrosine Kinase Inhibitors through Transition-State Effects.

Bravo Jr., E., Li, Y., Lin, D.Y., Srinivasan, B., Barone, M., Li, S.X., DelloRusso, F., Rahiyanath, A.S., Corrionero, A., Alfonso, P., Prendiville, N., Kozakov, D., Andreotti, A.H., Tonge, P.J.

(2025) J Am Chem Soc 147: 27876-27891

• PubMed: 40726426 
• DOI: https://doi.org/10.1021/jacs.5c07063
• Primary Citation Related Structures: 
  9EJJ, 9EJR, 9EJS, 9EJX, 9ME2, 9ME3


• PubMed Abstract: 
  

  Optimization exercises strive toward increasing the efficacy and selectivity of small molecules toward the target of interest while simultaneously phasing out design elements that lead to off-target interactions. Given the nonequilibrium nature of biological systems, greater reliance should be placed on engineering kinetic selectivity in addition to equilibrium thermodynamic selectivity; however, the rational design of kinetic selectivity is a challenging endeavor. This study presents a systematic knowledge-based approach to the design of inhibitors that vary in their binding kinetics for Bruton's tyrosine kinase (BTK), a target for treating B-cell malignancies and autoimmune diseases. A detailed kinetic assessment was performed on existing BTK inhibitors, which, together with structural studies, provided critical insights into BTK-inhibitor interactions that control the kinetics of enzyme inhibition. Subsequently, a series of pyrazolopyrimidines was designed with the objective of modifying interactions between the inhibitor and the regulatory (R) spine in the kinase back pocket, which were hypothesized to modulate the stability of the transition state on the binding reaction coordinate. This resulted in the development of BTK inhibitors with extended residence time in which the variation in k _on and k _off was uncoupled from equilibrium thermodynamic affinity.

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Organizational Affiliation: 
• Center for the Advanced Study of Drug Action, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States.
Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States.
Cancer Research Horizons, Cancer Research U.K., Cambridge CB2 0RE, U.K.
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794-3400, United States.
Enzymlogic S.L., QUBE Technology Park, C/Santiago Grisolía, 2, 28760 Madrid, Spain.
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States.
Department of Biomedical Genetics, University of Rochester, Rochester, New York 14642, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.12 kDa 
• Atom Count: 2,142 
• Modeled Residue Count: 265 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A	271	Mus musculus	Mutation(s): 8  Gene Names: Btk, Bpk EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P35991 (Mus musculus) Explore P35991  Go to UniProtKB:  P35991
IMPC:  MGI:88216

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BJE	B [auth A]	3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine C17 H13 N5 O YYVUOZULIDAKRN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.288 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.63	α = 90
b = 107.63	β = 90
c = 45.276	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Lin, D.Y., Andreotti, A.H., Tonge, P.J., Bravo, E., Li, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release
  
• Version 1.1: 2025-08-20
  Changes: Database references