5O1S

Dimethyl fumarate is an allosteric covalent inhibitor of the p90 ribosomal S6 kinases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dimethyl fumarate is an allosteric covalent inhibitor of the p90 ribosomal S6 kinases.

Andersen, J.L.Gesser, B.Funder, E.D.Nielsen, C.J.F.Gotfred-Rasmussen, H.Rasmussen, M.K.Toth, R.Gothelf, K.V.Arthur, J.S.C.Iversen, L.Nissen, P.

(2018) Nat Commun 9: 4344-4344

  • DOI: 10.1038/s41467-018-06787-w
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Dimethyl fumarate (DMF) has been applied for decades in the treatment of psoriasis and now also multiple sclerosis. However, the mechanism of action has remained obscure and involves high dose over long time of this small, reactive compound implicati ...

    Dimethyl fumarate (DMF) has been applied for decades in the treatment of psoriasis and now also multiple sclerosis. However, the mechanism of action has remained obscure and involves high dose over long time of this small, reactive compound implicating many potential targets. Based on a 1.9 Å resolution crystal structure of the C-terminal kinase domain of the mouse p90 Ribosomal S6 Kinase 2 (RSK2) inhibited by DMF we describe a central binding site in RSKs and the closely related Mitogen and Stress-activated Kinases (MSKs). DMF reacts covalently as a Michael acceptor to a conserved cysteine residue in the αF-helix of RSK/MSKs. Binding of DMF prevents the activation loop of the kinase from engaging substrate, and stabilizes an auto-inhibitory αL-helix, thus pointing to an effective, allosteric mechanism of kinase inhibition. The biochemical and cell biological characteristics of DMF inhibition of RSK/MSKs are consistent with the clinical protocols of DMF treatment.


    Organizational Affiliation

    Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000, Aarhus C, Denmark. pn@mbg.au.dk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S6 kinase alpha-3
A
364Mus musculusMutation(s): 0 
Gene Names: Rps6ka3Mapkapk1bRps6ka-rs1Rsk2
EC: 2.7.11.1
Find proteins for P18654 (Mus musculus)
Go to UniProtKB:  P18654
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9HB
Query on 9HB

Download CCD File 
A
Dimethyl fumarate
C6 H10 O4
MUXOBHXGJLMRAB-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.951α = 90
b = 46.951β = 90
c = 291.865γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo NordiskDenmark--

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection
  • Version 1.2: 2018-10-31
    Changes: Data collection, Database references