8OKU

Salt-Inducible Kinase 3 in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Optimization of Selectivity and Pharmacokinetic Properties of Salt-Inducible Kinase Inhibitors that Led to the Discovery of Pan-SIK Inhibitor GLPG3312.

Temal-Laib, T.Peixoto, C.Desroy, N.De Lemos, E.Bonnaterre, F.Bienvenu, N.Picolet, O.Sartori, E.Bucher, D.Lopez-Ramos, M.Roca Magadan, C.Laenen, W.Flower, T.Mollat, P.Bugaud, O.Touitou, R.Pereira Fernandes, A.Lavazais, S.Monjardet, A.Borgonovi, M.Gosmini, R.Brys, R.Amantini, D.De Vos, S.Andrews, M.

(2024) J Med Chem 67: 380-401

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01428
  • Primary Citation of Related Structures:  
    8OKU

  • PubMed Abstract: 

    Salt-inducible kinases (SIKs) SIK1, SIK2, and SIK3 are serine/threonine kinases and form a subfamily of the protein kinase AMP-activated protein kinase (AMPK) family. Inhibition of SIKs in stimulated innate immune cells and mouse models has been associated with a dual mechanism of action consisting of a reduction of pro-inflammatory cytokines and an increase of immunoregulatory cytokine production, suggesting a therapeutic potential for inflammatory diseases. Following a high-throughput screening campaign, subsequent hit to lead optimization through synthesis, structure-activity relationship, kinome selectivity, and pharmacokinetic investigations led to the discovery of clinical candidate GLPG3312 (compound 28 ), a potent and selective pan-SIK inhibitor (IC 50 : 2.0 nM for SIK1, 0.7 nM for SIK2, and 0.6 nM for SIK3). Characterization of the first human SIK3 crystal structure provided an understanding of the binding mode and kinome selectivity of the chemical series. GLPG3312 demonstrated both anti-inflammatory and immunoregulatory activities in vitro in human primary myeloid cells and in vivo in mouse models.


  • Organizational Affiliation

    Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase SIK3
A, B
348Homo sapiensMutation(s): 1 
Gene Names: SIK3KIAA0999QSKL19
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2K2 (Homo sapiens)
Explore Q9Y2K2 
Go to UniProtKB:  Q9Y2K2
PHAROS:  Q9Y2K2
GTEx:  ENSG00000160584 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2K2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VRU (Subject of Investigation/LOI)
Query on VRU

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
~{N}-ethyl-4-[5-[1-(2-hydroxyethyl)pyrazol-4-yl]benzimidazol-1-yl]-2,6-dimethoxy-benzamide
C23 H25 N5 O4
FCJGMZMSVIAAJU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.553α = 90
b = 174.553β = 90
c = 152.308γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Aimlessdata scaling
MOSFLMdata reduction
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Database references