4I0T

Crystal structure of spleen tyrosine kinase complexed with 2-(5,6,7,8-Tetrahydro-imidazo[1,5-a]pyridin-1-yl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid tert-butylamide

• PDB DOI: https://doi.org/10.2210/pdb4I0T/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-11-19 Released: 2013-10-30 
• Deposition Author(s): Kuglstatter, A., Slade, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.268 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 

Starting Model: experimental

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

• PubMed: 23350847 
• DOI: https://doi.org/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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.22 kDa 
• Atom Count: 2,344 
• Modelled Residue Count: 266 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	291	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1B6	B [auth A]	N-tert-butyl-2-(5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-1-yl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide C18 H22 N6 O NEVNJCLJFXHCCC-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1B6	BindingDB:  4I0T	IC50: min: 26, max: 634 (nM) from 3 assay(s)
	PDBBind:  4I0T	IC50: 26 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.268 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.854	α = 90
b = 87.405	β = 90
c = 88.867	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-30 
Deposition Author(s): Kuglstatter, A., Slade, M.

Revision History  

• Version 1.0: 2013-10-30
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description