Structure of RSK2 T493M CTD mutant bound to 2-cyano-N-(1-hydroxy-2-methylpropan-2-yl)-3-(3-(3,4,5-trimethoxyphenyl)-1H-indazol-5-yl)acrylamide

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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This is version 1.5 of the entry. See complete history


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: https://doi.org/10.1021/ja401221b
  • Primary Citation of Related Structures:  
    4JG6, 4JG7, 4JG8

  • 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-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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S6 kinase alpha-3355Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P51812 (Homo sapiens)
Explore P51812 
Go to UniProtKB:  P51812
PHAROS:  P51812
GTEx:  ENSG00000177189 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51812
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1LE

Download Ideal Coordinates CCD File 
B [auth A](2S)-2-cyano-N-(1-hydroxy-2-methylpropan-2-yl)-3-[3-(3,4,5-trimethoxyphenyl)-1H-indazol-5-yl]propanamide
C24 H28 N4 O5
Binding Affinity Annotations 
IDSourceBinding Affinity
1LE PDBBind:  4JG8 IC50: 2.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.35α = 90
b = 46.35β = 90
c = 292.36γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Database references
  • Version 1.2: 2013-04-24
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-09-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-12-27
    Changes: Derived calculations