3V8W

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


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

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

  • DOI: 10.1016/j.bmcl.2012.03.016
  • Primary Citation of Related Structures:  

  • 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 wer ...

    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.

    Organizational Affiliation: 

    Molecular Innovative Therapeutics, Sanofi US, 1041 Route 202/206 N, Bridgewater, NJ 08807, United States. Larry.McLean@sanofi.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase ITK/TSK
A, B
266Homo sapiensMutation(s): 0 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0G2
Query on 0G2
Download SDF File 
Download CCD File 
A, 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
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0G2IC50: 8.6 nM BINDINGMOAD
0G2IC50: 8.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.251 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.080α = 90.00
b = 69.290β = 108.04
c = 68.580γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
PHASERphasing
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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