3V5J

Crystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Catalytic Domain with Thienopyrazolylindole Inhibitor 090


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 

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:  
    3V8W, 3VF8, 3VF9, 3V5J, 3V5L, 3V8T

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase ITK/TSKAB266Homo sapiensMutation(s): 0 
Gene Names: ITKEMTLYK
EC: 2.7.10.2
Find proteins for Q08881 (Homo sapiens)
Explore Q08881 
Go to UniProtKB:  Q08881
NIH Common Fund Data Resources
PHAROS  Q08881
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0F2
Query on 0F2

Download CCD File 
A, B
3-[4-(2-morpholin-4-ylethoxy)-2-(1~{H}-thieno[3,2-c]pyrazol-3-yl)-1~{H}-indol-6-yl]pentan-3-ol
C24 H30 N4 O3 S
PVCKRSKEOOWVMP-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0F2IC50 :  10.899999618530273   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.132α = 90
b = 69.513β = 107.33
c = 68.244γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references, Derived calculations, Structure summary