5T68

Crystal structure of Syk catalytic domain in complex with a furo[3,2-d]pyrimidine

• PDB DOI: https://doi.org/10.2210/pdb5T68/pdb

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


• Deposited: 2016-09-01 Released: 2016-10-26 
• Deposition Author(s): Argiriadi, M.A., Hoemann, M., Wilson, N., Banach, D., Burchat, A., Calderwood, D., Clapham, B., Cox, P., Duignan, D.B., Konopacki, D., Somal, G., Vasudevan, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.93 Å
• R-Value Free: 0.281 
• R-Value Work: 0.183 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Synthesis and optimization of furano[3,2-d]pyrimidines as selective spleen tyrosine kinase (Syk) inhibitors.

Hoemann, M., Wilson, N., Argiriadi, M., Banach, D., Burchat, A., Calderwood, D., Clapham, B., Cox, P., Duignan, D.B., Konopacki, D., Somal, G., Vasudevan, A.

(2016) Bioorg Med Chem Lett 26: 5562-5567

• PubMed: 27789138 
• DOI: https://doi.org/10.1016/j.bmcl.2016.09.077
• Primary Citation of Related Structures:  
  5T68


• PubMed Abstract: 
  

  A series of furano[3,2-d]pyrimidine Syk inhibitors were synthesized and optimized for their enzyme potency and selectivity versus other kinases. In addition, ADME properties were assessed and compounds were prepared with optimized profiles for in vivo experiments. Compound 23 was identified as having acceptable pharmacokinetic properties and demonstrated efficacy in a rat collagen induced arthritis model.

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Organizational Affiliation: 

AbbVie Bioresearch Center, 100 Research Dr., Worcester, MA 01545, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 68.41 kDa 
• Atom Count: 4,224 
• Modelled Residue Count: 530 
• Deposited Residue Count: 582 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A, B	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
77V	C [auth A], D [auth B]	N~4~-cyclopropyl-N~2~-(3-methyl-1H-indazol-6-yl)furo[3,2-d]pyrimidine-2,4-diamine C17 H16 N6 O MDWXVGCLSBQVMP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
77V	BindingDB:  5T68	IC50: min: 23, max: 24 (nM) from 2 assay(s)
		EC50: 34 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.93 Å
• R-Value Free: 0.281 
• R-Value Work: 0.183 
• R-Value Observed: 0.188 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.605	α = 90.16
b = 40.03	β = 89.98
c = 84.046	γ = 99.8

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Argiriadi, M.A., Hoemann, M., Wilson, N., Banach, D., Burchat, A., Calderwood, D., Clapham, B., Cox, P., Duignan, D.B., Konopacki, D., Somal, G., Vasudevan, A.

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2016-11-16
  Changes: Database references
• Version 1.2: 2016-12-28
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Data collection
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description