3PIY

Crystal structure of BTK kinase domain complexed with R406

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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

  • DOI: 10.1002/pro.575
  • Primary Citation of Related Structures:  

  • 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 in ...

    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.

    Organizational Affiliation: 

    Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, California 94304, USA. andreas.kuglstatter@roche.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase BTK
A
274Homo sapiensMutation(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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
585
Query on 585
Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
585Kd: 190 nM (99) BINDINGDB
585IC50: 290 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.905α = 90.00
b = 105.013β = 90.00
c = 38.052γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
REFMACphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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