4M8T

RSK2 T493M C-Terminal Kinase Domain in complex with 3-(3-(1H-pyrazol-4-yl)phenyl)-2-cyanoacrylamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Covalent docking of large libraries for the discovery of chemical probes.

London, N.Miller, R.M.Krishnan, S.Uchida, K.Irwin, J.J.Eidam, O.Gibold, L.Cimermancic, P.Bonnet, R.Shoichet, B.K.Taunton, J.

(2014) Nat Chem Biol 10: 1066-1072

  • DOI: 10.1038/nchembio.1666
  • Primary Citation of Related Structures:  
    4LV0, 4LV1, 4LV2, 4LV3, 4M8T

  • PubMed Abstract: 
  • Chemical probes that form a covalent bond with a protein target often show enhanced selectivity, potency and utility for biological studies. Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaigns. Here we describe a general method (DOCKovalent) for screening large virtual libraries of electrophilic small molecules ...

    Chemical probes that form a covalent bond with a protein target often show enhanced selectivity, potency and utility for biological studies. Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaigns. Here we describe a general method (DOCKovalent) for screening large virtual libraries of electrophilic small molecules. We apply this method prospectively to discover reversible covalent fragments that target distinct protein nucleophiles, including the catalytic serine of AmpC β-lactamase and noncatalytic cysteines in RSK2, MSK1 and JAK3 kinases. We identify submicromolar to low-nanomolar hits with high ligand efficiency, cellular activity and selectivity, including what are to our knowledge the first reported reversible covalent inhibitors of JAK3. Crystal structures of inhibitor complexes with AmpC and RSK2 confirm the docking predictions and guide further optimization. As covalent virtual screening may have broad utility for the rapid discovery of chemical probes, we have made the method freely available through an automated web server (http://covalent.docking.org/).


    Organizational Affiliation

    1] Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA. [2] Howard Hughes Medical Institute, University of California-San Francisco, San Francisco, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S6 kinase alpha-3A355Mus musculusMutation(s): 1 
Gene Names: Rps6ka3Mapkapk1bRps6ka-rs1Rsk2
EC: 2.7.11.1
Find proteins for P18654 (Mus musculus)
Explore P18654 
Go to UniProtKB:  P18654
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RMM
Query on RMM

Download Ideal Coordinates CCD File 
B [auth A](2E)-2-cyano-3-[3-(1H-pyrazol-4-yl)phenyl]prop-2-enamide
C13 H10 N4 O
YCZXMEXRJXFIIS-VZUCSPMQSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.99α = 90
b = 46.99β = 90
c = 291.1γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references
  • Version 1.2: 2014-11-26
    Changes: Database references