8TXY

X-ray crystal structure of JRD-SIK1/2i-3 bound to a MARK2-SIK2 chimera


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.267 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

Starting Model: experimental
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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 SJ0Click on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Identification of highly selective SIK1/2 inhibitors that modulate innate immune activation and suppress intestinal inflammation.

Babbe, H.Sundberg, T.B.Tichenor, M.Seierstad, M.Bacani, G.Berstler, J.Chai, W.Chang, L.Chung, M.Coe, K.Collins, B.Finley, M.Guletsky, A.Lemke, C.T.Mak, P.A.Mathur, A.Mercado-Marin, E.V.Metkar, S.Raymond, D.D.Rives, M.L.Rizzolio, M.Shaffer, P.L.Smith, R.Smith, J.Steele, R.Steffens, H.Suarez, J.Tian, G.Majewski, N.Volak, L.P.Wei, J.Desai, P.T.Ong, L.L.Koudriakova, T.Goldberg, S.D.Hirst, G.Kaushik, V.K.Ort, T.Seth, N.Graham, D.B.Plevy, S.Venable, J.D.Xavier, R.J.Towne, J.E.

(2024) Proc Natl Acad Sci U S A 121: e2307086120-e2307086120

  • DOI: https://doi.org/10.1073/pnas.2307086120
  • Primary Citation of Related Structures:  
    8TXY

  • PubMed Abstract: 

    The salt-inducible kinases (SIK) 1-3 are key regulators of pro- versus anti-inflammatory cytokine responses during innate immune activation. The lack of highly SIK-family or SIK isoform-selective inhibitors suitable for repeat, oral dosing has limited the study of the optimal SIK isoform selectivity profile for suppressing inflammation in vivo. To overcome this challenge, we devised a structure-based design strategy for developing potent SIK inhibitors that are highly selective against other kinases by engaging two differentiating features of the SIK catalytic site. This effort resulted in SIK1/2-selective probes that inhibit key intracellular proximal signaling events including reducing phosphorylation of the SIK substrate cAMP response element binding protein (CREB) regulated transcription coactivator 3 (CRTC3) as detected with an internally generated phospho-Ser329-CRTC3-specific antibody. These inhibitors also suppress production of pro-inflammatory cytokines while inducing anti-inflammatory interleukin-10 in activated human and murine myeloid cells and in mice following a lipopolysaccharide challenge. Oral dosing of these compounds ameliorates disease in a murine colitis model. These findings define an approach to generate highly selective SIK1/2 inhibitors and establish that targeting these isoforms may be a useful strategy to suppress pathological inflammation.


  • Organizational Affiliation

    Janssen Research and Development, LLC., Spring House, PA 19477.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase MARK2
A, B
317Homo sapiensMutation(s): 9 
Gene Names: MARK2EMK1
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q7KZI7 (Homo sapiens)
Explore Q7KZI7 
Go to UniProtKB:  Q7KZI7
PHAROS:  Q7KZI7
GTEx:  ENSG00000072518 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7KZI7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SJ0 (Subject of Investigation/LOI)
Query on SJ0

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
N-[(5P,8R)-5-(2-cyano-5-{[(3R)-1-methylpyrrolidin-3-yl]methoxy}pyridin-4-yl)pyrazolo[1,5-a]pyridin-2-yl]cyclopropanecarboxamide
C23 H24 N6 O2
GMHAIVQASIBHJM-OAHLLOKOSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.267 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.43α = 90
b = 121.43β = 90
c = 99.64γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

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 SJ0Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Structure summary