4I0R

Crystal structure of spleen tyrosine kinase complexed with 2-(3,4,5-Trimethoxy-phenyl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid isopropylamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Pyrrolopyrazines as selective spleen tyrosine kinase inhibitors.

Padilla, F.Bhagirath, N.Chen, S.Chiao, E.Goldstein, D.M.Hermann, J.C.Hsu, J.Kennedy-Smith, J.J.Kuglstatter, A.Liao, C.Liu, W.Lowrie, L.E.Luk, K.C.Lynch, S.M.Menke, J.Niu, L.Owens, T.D.O-Yang, C.Railkar, A.Schoenfeld, R.C.Slade, M.Steiner, S.Tan, Y.C.Villasenor, A.G.Wang, C.Wanner, J.Xie, W.Xu, D.Zhang, X.Zhou, M.Lucas, M.C.

(2013) J Med Chem 56: 1677-1692

  • DOI: 10.1021/jm301720p
  • Primary Citation of Related Structures:  
    4I0R, 4I0S, 4I0T

  • PubMed Abstract: 
  • We describe the discovery of several pyrrolopyrazines as potent and selective Syk inhibitors and the efforts that eventually led to the desired improvements in physicochemical properties and human whole blood potencies. Ultimately, our mouse model revealed unexpected toxicity that precluded us from further advancing this series ...

    We describe the discovery of several pyrrolopyrazines as potent and selective Syk inhibitors and the efforts that eventually led to the desired improvements in physicochemical properties and human whole blood potencies. Ultimately, our mouse model revealed unexpected toxicity that precluded us from further advancing this series.


    Organizational Affiliation

    Hoffmann-La Roche Inc., pRED, Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYKA291Homo 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1B4 (Subject of Investigation/LOI)
Query on 1B4

Download Ideal Coordinates CCD File 
B [auth A]N-(propan-2-yl)-2-(3,4,5-trimethoxyphenyl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide
C19 H22 N4 O4
WWUBOSRORWJGRU-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1B4 PDBBind:  4I0R IC50: 14 (nM) from 1 assay(s)
BindingDB:  4I0R IC50: min: 14, max: 7090 (nM) from 3 assay(s)
Binding MOAD:  4I0R IC50: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.785α = 90
b = 85.118β = 90
c = 90.158γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Refinement description