6SSB

syk in complex with compound 30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.225 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LUEClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Discovery of a Series of Potent, Selective and Orally Bioavailable SYK Inhibitors

Read, J.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYK299Homo 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
LUE (Subject of Investigation/LOI)
Query on LUE

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[4-[5-[(dimethylamino)methyl]-1-methyl-pyrazol-3-yl]pyrimidin-2-yl]-3-methyl-1-(5-methyl-1,3,4-oxadiazol-2-yl)imidazo[1,5-a]pyridin-7-amine
C22 H24 N10 O
PAZNLQHSWVMGIW-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
LUE BindingDB:  6SSB IC50: 0.19 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.225 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.1α = 90
b = 85.45β = 90
c = 90.57γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LUEClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2020-09-30 
  • Deposition Author(s): Read, J.A.

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references