Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.30 kDa 
• Atom Count: 2226 
• Modelled Residue Count: 262 
• Deposited Residue Count: 274 
• Unique protein chains: 1

3PIY

Crystal structure of BTK kinase domain complexed with R406

• PDB DOI: 10.2210/pdb3PIY/pdb

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


• Deposited: 2010-11-08 Released: 2011-01-12 
• Deposition Author(s): Kuglstatter, A., Wong, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.295 
• R-Value Work: 0.225 
• R-Value Observed: 0.228 

Literature

Insights into the conformational flexibility of Bruton's tyrosine kinase from multiple ligand complex structures.

Kuglstatter, A., Wong, A., Tsing, S., Lee, S.W., Lou, Y., Villasenor, A.G., Bradshaw, J.M., Shaw, D., Barnett, J.W., Browner, M.F.

(2011) Protein Sci 20: 428-436

• PubMed: 21280133 
• DOI: 10.1002/pro.575
• Primary Citation of Related Structures:  
  3PIX, 3PIY, 3PIZ, 3PJ1, 3PJ2, 3PJ3


• PubMed Abstract: 
  

Bruton's tyrosine kinase (BTK) plays a key role in B cell receptor signaling and is considered a promising drug target for lymphoma and inflammatory diseases. We have determined the X-ray crystal structures of BTK kinase domain in complex with six inhibitors from distinct chemical classes. Five different BTK protein conformations are stabilized by the bound inhibitors, providing insights into the structural flexibility of the Gly-rich loop, helix C, the DFG sequence, and activation loop. The conformational changes occur independent of activation loop phosphorylation and do not correlate with the structurally unchanged WEI motif in the Src homology 2-kinase domain linker. Two novel activation loop conformations and an atypical DFG conformation are observed representing unique inactive states of BTK. Two regions within the activation loop are shown to structurally transform between 3(10)- and α-helices, one of which collapses into the adenosine-5'-triphosphate binding pocket. The first crystal structure of a Tec kinase family member in the pharmacologically important DFG-out conformation and bound to a type II kinase inhibitor is described. The different protein conformations observed provide insights into the structural flexibility of BTK, the molecular basis of its regulation, and the structure-based design of specific inhibitors.

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Organizational Affiliation: 

Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, California 94304, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A	274	Homo sapiens	Mutation(s): 0  Gene Names: AGMX1, ATK, BPK, BTK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens) Explore Q06187  Go to UniProtKB:  Q06187
PHAROS:  Q06187

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
585	B [auth A]	6-({5-fluoro-2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}amino)-2,2-dimethyl-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one C22 H23 F N6 O5 NHHQJBCNYHBUSI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
585	BindingDB:  3PIY	Kd: 190 (nM) from 1 assay(s)
	PDBBind:  3PIY	IC50: 290 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.295 
• R-Value Work: 0.225 
• R-Value Observed: 0.228 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.905	α = 90
b = 105.013	β = 90
c = 38.052	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-08 
• Released Date: 2011-01-12 
Deposition Author(s): Kuglstatter, A., Wong, A.

Revision History  

• Version 1.0: 2011-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance