5LMB

HUMAN SPLEEN TYROSINE KINASE KINASE DOMAIN IN COMPLEX WITH AZANAPHTHYRIDINE INHIBITOR

• PDB DOI:  https://doi.org/10.2210/pdb5LMB/pdb

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


• Deposited: 2016-07-29 Released: 2016-09-14 
• Deposition Author(s): Somers, D.O., Neu, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.228 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 

Literature

Optimisation of a novel series of potent and orally bioavailable azanaphthyridine SYK inhibitors.

Garton, N.S., Barker, M.D., Davis, R.P., Douault, C., Hooper-Greenhill, E., Jones, E., Lewis, H.D., Liddle, J., Lugo, D., McCleary, S., Preston, A.G., Ramirez-Molina, C., Neu, M., Shipley, T.J., Somers, D.O., Watson, R.J., Wilson, D.M.

(2016) Bioorg Med Chem Lett 26: 4606-4612

• PubMed: 27578246 
• DOI: https://doi.org/10.1016/j.bmcl.2016.08.070
• Primary Citation of Related Structures:  
  5LMA, 5LMB


• PubMed Abstract: 
  

The optimisation of the azanaphthyridine series of Spleen Tyrosine Kinase inhibitors is described. The medicinal chemistry strategy was focused on optimising the human whole blood activity whilst achieving a sufficient margin over hERG activity. A good pharmacokinetic profile was achieved by modification of the pKa. Morpholine compound 32 is a potent SYK inhibitor showing moderate selectivity, good oral bioavailability and good efficacy in the rat Arthus model but demonstrated a genotoxic potential in the Ames assay.

---

Organizational Affiliation: 

AstraZeneca, Hodgkin Building, Chesterford Research Campus, Little Chesterford, Saffron Walden, Cambs. CB10 1XL, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.7 kDa 
• Atom Count: 4,811 
• Modelled Residue Count: 527 
• Deposited Residue Count: 554 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A, B	277	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6ZF	C [auth A], I [auth B]	7-[6-(dimethylamino)pyridin-3-yl]-~{N}-[[(3~{S})-piperidin-3-yl]methyl]pyrido[3,4-b]pyrazin-5-amine C20 H25 N7 CLKZDZYGBHNPSM-AWEZNQCLSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
6ZF	Binding MOAD:  5LMB	IC50: 16 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.228 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.849	α = 99.81
b = 41.78	β = 90.41
c = 86.991	γ = 100.03

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Somers, D.O., Neu, M.

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Database references
• Version 1.2: 2019-04-03
  Changes: Data collection, Source and taxonomy