6HM6

CRYSTAL STRUCTURE OF SPLEEN TYROSINE KINASE (SYK) IN COMPLEX WITH A 2-(PYRIDINYLOXYMETHYL)PYRIDINE INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb6HM6/pdb

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


• Deposited: 2018-09-12 Released: 2018-10-10 
• Deposition Author(s): Somers, D.O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.290 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 

Starting Model: other

Literature

Discovery of potent and selective Spleen Tyrosine Kinase inhibitors for the topical treatment of inflammatory skin disease.

Barker, M.D., Liddle, J., Atkinson, F.L., Wilson, D.M., Dickson, M.C., Ramirez-Molina, C., Lewis, H., Davis, R.P., Somers, D.O., Neu, M., Jones, E., Watson, R.

(2018) Bioorg Med Chem Lett 28: 3458-3462

• PubMed: 30249354 
• DOI: https://doi.org/10.1016/j.bmcl.2018.09.022
• Primary Citation of Related Structures:  
  6HM6, 6HM7


• PubMed Abstract: 
  

  The discovery and lead optimisation of a novel series of SYK inhibitors is described. These were optimised for SYK potency and selectivity against Aurora B. Compounds were profiled in a human skin penetration study to identify a suitable candidate molecule for pre-clinical development. Compound 44 (GSK2646264) was selected for progression and is currently in Phase I clinical trials.

---

Organizational Affiliation: 

GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.47 kDa 
• Atom Count: 2,276 
• Modelled Residue Count: 261 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPLEEN TYROSINE KINASE	A	276	Homo sapiens	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDK	B [auth A]	2-(4-methylphenyl)-3-(pyridin-2-ylmethoxy)pyridine C18 H16 N2 O GEICNUUKZLWKET-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
GDK	BindingDB:  6HM6	IC50: 3162 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.290 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.437	α = 90
b = 84.982	β = 100.5
c = 40.277	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data reduction
d*TREK	data scaling
PDB_EXTRACT	data extraction
REFMAC	phasing
REFMAC	refinement
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Somers, D.O.

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2018-10-17
  Changes: Data collection, Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary