4MAO

RSK2 T493M C-Terminal Kinase Domain in Complex with RMM58


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis.

Krishnan, S.Miller, R.M.Tian, B.Mullins, R.D.Jacobson, M.P.Taunton, J.

(2014) J.Am.Chem.Soc. 136: 12624-12630

  • DOI: 10.1021/ja505194w

  • PubMed Abstract: 
  • Electrophilic probes that covalently modify a cysteine thiol often show enhanced pharmacological potency and selectivity. Although reversible Michael acceptors have been reported, the structural requirements for reversibility are poorly understood. H ...

    Electrophilic probes that covalently modify a cysteine thiol often show enhanced pharmacological potency and selectivity. Although reversible Michael acceptors have been reported, the structural requirements for reversibility are poorly understood. Here, we report a novel class of acrylonitrile-based Michael acceptors, activated by aryl or heteroaryl electron-withdrawing groups. We demonstrate that thiol adducts of these acrylonitriles undergo β-elimination at rates that span more than 3 orders of magnitude. These rates correlate inversely with the computed proton affinity of the corresponding carbanions, enabling the intrinsic reversibility of the thiol-Michael reaction to be tuned in a predictable manner. We apply these principles to the design of new reversible covalent kinase inhibitors with improved properties. A cocrystal structure of one such inhibitor reveals specific noncovalent interactions between the 1,2,4-triazole activating group and the kinase. Our experimental and computational study enables the design of new Michael acceptors, expanding the palette of reversible, cysteine-targeted electrophiles.


    Organizational Affiliation

    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California-San Francisco , San Francisco, California 94158, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S6 kinase alpha-3
A
355Mus musculusMutation(s): 2 
Gene Names: Rps6ka3 (Mapkapk1b, Rps6ka-rs1, Rsk2)
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
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
28D
Query on 28D

Download SDF File 
Download CCD File 
A
(2Z)-2-(1H-1,2,4-triazol-1-yl)-3-[3-(3,4,5-trimethoxyphenyl)-1H-indazol-5-yl]prop-2-enenitrile
C21 H18 N6 O3
KVQZHZNPPJMLLH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.235 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.500α = 90.00
b = 47.500β = 90.00
c = 288.500γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
XDSdata reduction
PHENIXphasing
Blu-Icedata collection
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release