4PX6

SYK catalytic domain in complex with a potent pyridopyrimidinone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4PX6/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2014-03-21 Released: 2014-04-23 
• Deposition Author(s): Lee, C.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.202 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Starting Model: experimental

Literature

Syk inhibitors with high potency in presence of blood.

Thoma, G., Blanz, J., Buhlmayer, P., Druckes, P., Kittelmann, M., Smith, A.B., van Eis, M., Vangrevelinghe, E., Zerwes, H.G., Che, J.J., He, X., Jin, Y., Lee, C.C., Michellys, P.Y., Uno, T., Liu, H.

(2014) Bioorg Med Chem Lett 24: 2278-2282

• PubMed: 24726806 
• DOI: https://doi.org/10.1016/j.bmcl.2014.03.075
• Primary Citation of Related Structures:  
  4PX6


• PubMed Abstract: 
  

  We describe two series of Syk inhibitors which potently abrogate Syk kinase function in enzymatic assays, cellular assays and in primary cells in the presence of blood. Introduction of a 7-aminoindole substituent led to derivatives with good kinase selectivity and little or no hERG channel inhibition (3b, 10c).

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Organizational Affiliation: 

Novartis Institutes for Biomedical Research, Forum 1 Novartis Campus, 4056 Basel, Switzerland. Electronic address: [e-mail].

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: 34.25 kDa 
• Atom Count: 2,376 
• Modelled Residue Count: 262 
• 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): 1  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
2X6	B [auth A]	7-{[(1R,2S)-2-aminocyclohexyl]amino}-5-(1H-indol-7-ylamino)pyrido[4,3-d]pyrimidin-4(3H)-one C21 H23 N7 O JZLUCFJMWJDRIK-UONOGXRCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2X6	BindingDB:  4PX6	IC50: min: 4, max: 307 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.202 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.889	α = 90
b = 85.161	β = 90
c = 88.961	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BUSTER	refinement
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-23 
Deposition Author(s): Lee, C.C.

Revision History  

• Version 1.0: 2014-04-23
  Type: Initial release
  
• Version 1.1: 2014-05-21
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description