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.

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.40 kDa 
• Atom Count: 3792 
• Modelled Residue Count: 485 
• Deposited Residue Count: 532 
• Unique protein chains: 1

3V8W

Crystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Catalytic Domain with Thienopyrazolylindole Inhibitor 469

• PDB DOI: 10.2210/pdb3V8W/pdb

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


• Deposited: 2011-12-23 Released: 2012-05-02 
• Deposition Author(s): McLean, L.R., Zhang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.268 
• R-Value Work: 0.251 
• R-Value Observed: 0.252 

Literature

X-ray crystallographic structure-based design of selective thienopyrazole inhibitors for interleukin-2-inducible tyrosine kinase.

McLean, L.R., Zhang, Y., Zaidi, N., Bi, X., Wang, R., Dharanipragada, R., Jurcak, J.G., Gillespy, T.A., Zhao, Z., Musick, K.Y., Choi, Y.M., Barrague, M., Peppard, J., Smicker, M., Duguid, M., Parkar, A., Fordham, J., Kominos, D.

(2012) Bioorg Med Chem Lett 22: 3296-3300

• PubMed: 22464456 
• DOI: 10.1016/j.bmcl.2012.03.016
• Primary Citation of Related Structures:  
  3V5J, 3V5L, 3V8T, 3V8W, 3VF8, 3VF9


• PubMed Abstract: 
  

Beginning with a screening hit, unique thienopyrazole-indole inhibitors of Itk (interleukin-2-inducible tyrosine kinase) were designed, synthesized, and crystallized in the target kinase. Although initial compounds were highly active in Itk, they were not selective. Increasing the steric bulk around a tertiary alcohol at the 5-indole position dramatically improved selectivity toward Lyk and Syk, but not Txk. Substitutions at the 3- and 4-indole positions gave less active compounds that remained poorly selective. A difluoromethyl substitution at the 5-position of the thienopyrazole led to a highly potent and selective compound. Phenyl at this position reduced activity and selectivity while pushing the side-chains of Lys-391 and Asp-500 away from the binding pocket. Novel and selective thienopyrazole inhibitors of Itk were designed as a result of combining structure-based design and medicinal chemistry.

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Organizational Affiliation: 

Molecular Innovative Therapeutics, Sanofi US, 1041 Route 202/206 N, Bridgewater, NJ 08807, United States. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ITK/TSK	A, B	266	Homo sapiens	Mutation(s): 0  Gene Names: ITK, EMT, 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0G2	C [auth A], E [auth B]	3-[2-(5-phenyl-2H-thieno[3,2-c]pyrazol-3-yl)-1H-indol-6-yl]pentan-3-ol C24 H23 N3 O S YBKODNZGBUDZRA-UHFFFAOYSA-N
SO4	D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
0G2	Binding MOAD:  3V8W	IC50: 8.6 (nM) from 1 assay(s)
	PDBBind:  3V8W	IC50: 8.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.268 
• R-Value Work: 0.251 
• R-Value Observed: 0.252 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.08	α = 90
b = 69.29	β = 108.04
c = 68.58	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
DENZO	data reduction
PHASER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-23 
• Released Date: 2012-05-02 
Deposition Author(s): McLean, L.R., Zhang, Y.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description