3VF9 | pdb_00003vf9

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 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 477Click on this verticalbar to view details

This is version 1.2 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: https://doi.org/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.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYK299Homo sapiensMutation(s): 0 
Gene Names: SYK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens)
Explore P43405 
Go to UniProtKB:  P43405
PHAROS:  P43405
GTEx:  ENSG00000165025 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43405
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
477
Query on 477

Download Ideal Coordinates CCD File 
B [auth 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.267 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
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



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 477Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations