4RSS

Crystal structure of tyrosine-protein kinase SYK with an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4RSS/pdb

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


• Deposited: 2014-11-11 Released: 2015-10-21 
• Deposition Author(s): Lee, B.I., Lee, S.J., Choi, J.-S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.249 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Literature

Highly potent and selective pyrazolylpyrimidines as Syk kinase inhibitors.

Choi, J.S., Hwang, H.J., Kim, S.W., Lee, B.I., Lee, J., Song, H.J., Koh, J.S., Kim, J.H., Lee, P.H.

(2015) Bioorg Med Chem Lett 25: 4441-4446

• PubMed: 26384287 
• DOI: https://doi.org/10.1016/j.bmcl.2015.09.011
• Primary Citation of Related Structures:  
  4RSS


• PubMed Abstract: 
  

  A series of pyrazolylpyrimidine scaffold based Syk inhibitors were synthesized and evaluated for their biological activities and selectivity. Lead optimization efforts provided compounds with potent Syk inhibition in both enzymatic and TNF-α release assay.

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Organizational Affiliation: 

Department of Chemistry, Kangwon National University, Chuncheon 200-701, Republic of Korea; Oscotec Inc., 694-1 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463-400, Republic of Korea.

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: 34.32 kDa 
• Atom Count: 2,414 
• Modelled Residue Count: 269 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	290	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
4MG	B [auth A]	1-[(3-methyl-1-{2-[(1,2,3-trimethyl-1H-indol-5-yl)amino]pyrimidin-4-yl}-1H-pyrazol-4-yl)methyl]azetidin-3-ol C23 H27 N7 O WVDKJJLIGILVRJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4MG	BindingDB:  4RSS	IC50: min: 1.7, max: 56 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.249 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.964	α = 90
b = 88.281	β = 91.48
c = 40.85	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Lee, B.I., Lee, S.J., Choi, J.-S.

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations