8TXY | pdb_00008txy

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), 0.243 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 74.69 kDa 
  • Atom Count: 5,160 
  • Modeled Residue Count: 610 
  • Deposited Residue Count: 634 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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), 0.243 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.229 (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 


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