4RSS

Crystal structure of tyrosine-protein kinase SYK with an inhibitor


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • 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.


  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYK290Homo 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
GTEx:  ENSG00000165025 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43405
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4MG
Query on 4MG

Download Ideal Coordinates CCD File 
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 
IDSourceBinding 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 = 39.964α = 90
b = 88.281β = 91.48
c = 40.85γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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