4MF0 | pdb_00004mf0

ITK kinase domain in complex with benzothiazole inhibitor compound 12a (1S,2S)-2-{4-[(DIMETHYLAMINO)METHYL]PHENYL}-N-[6-(PYRIDIN-3-YL)-1,3-BENZOTHIAZOL-2-YL]CYCLOPROPANECARBOXAMIDE (12a)

• PDB DOI: https://doi.org/10.2210/pdb4MF0/pdb

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


• Deposited: 2013-08-27 Released: 2013-11-13 
• Deposition Author(s): Eigenbrot, C., Shia, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 
  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Structure-based design and synthesis of potent benzothiazole inhibitors of interleukin-2 inducible T cell kinase (ITK).

Mackinnon, C.H., Lau, K., Burch, J.D., Chen, Y., Dines, J., Ding, X., Eigenbrot, C., Heifetz, A., Jaochico, A., Johnson, A., Kraemer, J., Kruger, S., Krulle, T.M., Liimatta, M., Ly, J., Maghames, R., Montalbetti, C.A., Ortwine, D.F., Perez-Fuertes, Y., Shia, S., Stein, D.B., Trani, G., Vaidya, D.G., Wang, X., Bromidge, S.M., Wu, L.C., Pei, Z.

(2013) Bioorg Med Chem Lett 23: 6331-6335

• PubMed: 24138940 
• DOI: https://doi.org/10.1016/j.bmcl.2013.09.069
• Primary Citation Related Structures: 
  4MF0, 4MF1


• PubMed Abstract: 
  

  Inhibition of the non-receptor tyrosine kinase ITK, a component of the T-cell receptor signalling cascade, may represent a novel treatment for allergic asthma. Here we report the structure-based optimization of a series of benzothiazole amides that demonstrate sub-nanomolar inhibitory potency against ITK with good cellular activity and kinase selectivity. We also elucidate the binding mode of these inhibitors by solving the X-ray crystal structures of several inhibitor-ITK complexes.

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Organizational Affiliation: 
• Evotec (UK) Ltd, 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 61.29 kDa 
• Atom Count: 3,904 
• Modeled Residue Count: 477 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ITK/TSK	A, B	266	Homo sapiens	Mutation(s): 1  Gene Names: EMT, ITK, LYK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q08881 (Homo sapiens) Explore Q08881  Go to UniProtKB:  Q08881
PHAROS:  Q08881 GTEx:  ENSG00000113263

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
29Z	C [auth A], D [auth B]	(1S,2S)-2-{4-[(dimethylamino)methyl]phenyl}-N-[6-(pyridin-3-yl)-1,3-benzothiazol-2-yl]cyclopropanecarboxamide C25 H24 N4 O S PGABPPHMLFSKKA-RTWAWAEBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free:  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.145	α = 90
b = 155.488	β = 93.74
c = 47.257	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-13 
Deposition Author(s): Eigenbrot, C., Shia, S.

Revision History  

• Version 1.0: 2013-11-13
  Type: Initial release
  
• Version 1.1: 2013-11-20
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations