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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31172.63 
• Atom Count: 2166 
• Residue Count: 269 
• Unique protein chains: 1

4HCT

Crystal structure of ITK in complex with compound 52

• DOI: 10.2210/pdb4HCT/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): 1 


• Deposited: 2012-10-01 Released: 2012-11-14 
• Deposition Author(s): Zapf, C.W., Gerstenberger, B.S., Xing, L., Limburg, D.C., Anderson, D.R., Caspers, N., Han, S., Aulabaugh, A., Kurumbail, R., Shakya, S., Li, X., Spaulding, V., Czerwinski, R.M., Seth, N., Medley, Q.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.184 
• R-Value Work: 0.171 

Literature

Covalent inhibitors of interleukin-2 inducible T cell kinase (itk) with nanomolar potency in a whole-blood assay.

Zapf, C.W., Gerstenberger, B.S., Xing, L., Limburg, D.C., Anderson, D.R., Caspers, N., Han, S., Aulabaugh, A., Kurumbail, R., Shakya, S., Li, X., Spaulding, V., Czerwinski, R.M., Seth, N., Medley, Q.G.

(2012) J.Med.Chem. 55: 10047-10063

• PubMed: 23098091 
• DOI: 10.1021/jm301190s
• Primary Citation of Related Structures:  
  4HCV, 4HCU


• PubMed Abstract: 
  

We wish to report a strategy that targets interleukin-2 inducible T cell kinase (Itk) with covalent inhibitors. Thus far, covalent inhibition of Itk has not been disclosed in the literature. Structure-based drug design was utilized to achieve low nanomolar potency of the disclosed series even at high ATP concentrations. Kinetic measurements confirmed an irreversible binding mode with off-rate half-lives exceeding 24 h and moderate on-rates. The analogues are highly potent in a cellular IP1 assay as well as in a human whole-blood (hWB) assay. Despite a half-life of approximately 2 h in resting primary T cells, the covalent inhibition of Itk resulted in functional silencing of the TCR pathway for more than 24 h. This prolonged effect indicates that covalent inhibition is a viable strategy to target the inactivation of Itk.

---

Organizational Affiliation: 

BioTherapeutics Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tyrosine-protein kinase ITK/TSK	A	269	Homo sapiens	Mutation(s): 1  Gene Names: ITK (EMT, LYK) EC: 2.7.10.2
Find proteins for Q08881 (Homo sapiens) Go to Gene View: ITK Go to UniProtKB:  Q08881

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
18R	A	3-{1-[(3R)-1-acryloylpiperidin-3-yl]-4-amino-1H-pyrazolo[3,4-d]pyrimidin-3-yl}-N-(3-tert-butylphenyl)benzamide C30 H33 N7 O2 RMAUIYTVKFMOGP-HSZRJFAPSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
18R	IC50: 10 - 2210 nM (99) BINDINGDB
18R	IC50: 73 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.184 
• R-Value Work: 0.171 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 41.410	α = 90.00
b = 67.850	β = 111.23
c = 49.280	γ = 90.00

Software Package:

Software Name	Purpose
BUSTER	refinement
SCALA	data scaling
AutoPROC	data scaling
AutoPROC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-01 
• Released Date: 2012-11-14 
• Deposition Author(s): Zapf, C.W., Gerstenberger, B.S., Xing, L., Limburg, D.C., Anderson, D.R., Caspers, N., Han, S., Aulabaugh, A., Kurumbail, R., Shakya, S., Li, X., Spaulding, V., Czerwinski, R.M., Seth, N., Medley, Q.G.

Revision History 

• Version 1.0: 2012-11-14
  Type: Initial release
• Version 1.1: 2013-01-02
  Type: Database references