5C26

Crystal structure of SYK in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Imidazotriazines: Spleen Tyrosine Kinase (Syk) Inhibitors Identified by Free-Energy Perturbation (FEP).

Lovering, F.Aevazelis, C.Chang, J.Dehnhardt, C.Fitz, L.Han, S.Janz, K.Lee, J.Kaila, N.McDonald, J.Moore, W.Moretto, A.Papaioannou, N.Richard, D.Ryan, M.S.Wan, Z.K.Thorarensen, A.

(2016) ChemMedChem 11: 217-233

  • DOI: 10.1002/cmdc.201500333
  • Primary Citation of Related Structures:  
    5C26, 5C27

  • PubMed Abstract: 
  • There has been significant interest in spleen tyrosine kinase (Syk) owing to its role in a number of disease states, including autoimmunity, inflammation, and cancer. Ongoing therapeutic programs have resulted in several compounds that are now in clinical use ...

    There has been significant interest in spleen tyrosine kinase (Syk) owing to its role in a number of disease states, including autoimmunity, inflammation, and cancer. Ongoing therapeutic programs have resulted in several compounds that are now in clinical use. Herein we report our optimization of the imidazopyrazine core scaffold of Syk inhibitors through the use of empirical and computational approaches. Free-energy perturbation (FEP) methods with MCPRO+ were undertaken to calculate the relative binding free energies for several alternate scaffolds. FEP was first applied retrospectively to determine if there is any predictive value; this resulted in 12 of 13 transformations being predicted in a directionally correct manner. FEP was then applied in a prospective manner to evaluate 17 potential targets, resulting in the realization of imidazotriazine 17 (3-(4-(3,4-dimethoxyphenylamino)imidazo[1,2-f][1,2,4]triazin-2-yl)benzamide), which shows a tenfold improvement in activity relative to the parent compound and no increase in atom count. Optimization of 17 led to compounds with nanomolar cellular activity.


    Organizational Affiliation

    Worldwide Medicinal Chemistry, Pfizer Worldwide R&D, 610 Main Street, Cambridge, MA, 02139, USA.



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
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens)
Explore P43405 
Go to UniProtKB:  P43405
PHAROS:  P43405
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GLU-VAL-PTR-GLU-SER-PROB6Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
50H (Subject of Investigation/LOI)
Query on 50H

Download Ideal Coordinates CCD File 
C [auth A]3-{8-[(3,4-dimethoxyphenyl)amino]imidazo[1,2-a]pyrazin-6-yl}benzamide
C21 H19 N5 O3
QJHCMTUHZIJSPR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
AL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
50H BindingDB:  5C26 IC50: 27 (nM) from 1 assay(s)
EC50: 244 (nM) from 1 assay(s)
Binding MOAD:  5C26 IC50: 170 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.99α = 90
b = 85.72β = 90
c = 89.96γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
SCALAdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2015-06-15 
  • Released Date: 2015-10-07 
  • Deposition Author(s): Han, S., Chang, J.

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references