4JG7

Structure of RSK2 CTD bound to 3-(3-(1H-pyrrolo[2,3-b]pyridine-3-carbonyl)phenyl)-2-cyanoacrylamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0002 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Electrophilic fragment-based design of reversible covalent kinase inhibitors.

Miller, R.M.Paavilainen, V.O.Krishnan, S.Serafimova, I.M.Taunton, J.

(2013) J.Am.Chem.Soc. 135: 5298-5301

  • DOI: 10.1021/ja401221b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fragment-based ligand design and covalent targeting of noncatalytic cysteines have been employed to develop potent and selective kinase inhibitors. Here, we combine these approaches, starting with a panel of low-molecular-weight, heteroaryl-susbstitu ...

    Fragment-based ligand design and covalent targeting of noncatalytic cysteines have been employed to develop potent and selective kinase inhibitors. Here, we combine these approaches, starting with a panel of low-molecular-weight, heteroaryl-susbstituted cyanoacrylamides, which we have previously shown to form reversible covalent bonds with cysteine thiols. Using this strategy, we identify electrophilic fragments with sufficient ligand efficiency and selectivity to serve as starting points for the first reported inhibitors of the MSK1 C-terminal kinase domain. Guided by X-ray co-crystal structures, indazole fragment 1 was elaborated to afford 12 (RMM-46), a reversible covalent inhibitor that exhibits high ligand efficiency and selectivity for MSK/RSK-family kinases. At nanomolar concentrations, 12 blocked activation of cellular MSK and RSK, as well as downstream phosphorylation of the critical transcription factor, CREB.


    Organizational Affiliation

    Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California 94158, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S6 kinase alpha-3
A
355Homo sapiensMutation(s): 0 
Gene Names: RPS6KA3 (ISPK1, MAPKAPK1B, RSK2)
EC: 2.7.11.1
Find proteins for P51812 (Homo sapiens)
Go to Gene View: RPS6KA3
Go to UniProtKB:  P51812
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
1LC
Query on 1LC

Download SDF File 
Download CCD File 
A
(2R)-2-cyano-3-[3-(1H-pyrrolo[2,3-b]pyridin-3-ylcarbonyl)phenyl]propanamide
C18 H14 N4 O2
UQJDULLQUOPWND-CYBMUJFWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1LCIC50: 120 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0002 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.259 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.660α = 90.00
b = 47.660β = 90.00
c = 292.120γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Database references
  • Version 1.2: 2013-04-24
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description