3VF9

Crystal Structure of Spleen Tyrosine Kinase Syk Catalytic Domain with Thienopyrazolylindole Inhibitor 027


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

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:  
    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 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 SYKA299Homo sapiensMutation(s): 0 
Gene Names: SYK
EC: 2.7.10.2
Find proteins for P43405 (Homo sapiens)
Explore P43405 
Go to UniProtKB:  P43405
NIH Common Fund Data Resources
PHAROS  P43405
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
477
Query on 477

Download CCD File 
A
3-{2-[5-(difluoromethyl)-2H-thieno[3,2-c]pyrazol-3-yl]-1H-indol-6-yl}pentan-3-ol
C19 H19 F2 N3 O S
CQZZZUNOWZUNNG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
477IC50 :  1.899999976158142   nM  PDBBind
477IC50:  358.20001220703125   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.813α = 90
b = 84.739β = 90
c = 90.184γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction
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: 2017-11-15
    Changes: Refinement description