4JG6

RSK2 CTD bound to 2-cyano-3-(1H-indazol-5-yl)acrylamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 

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This is version 1.2 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:  
    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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S6 kinase alpha-3A355Homo sapiensMutation(s): 0 
Gene Names: RPS6KA3, ISPK1, MAPKAPK1B, RSK2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P51812 (Homo sapiens)
Explore P51812 
Go to UniProtKB:  P51812
PHAROS:  P51812
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51812
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1LB
Query on 1LB
Download Ideal Coordinates CCD File 
B [auth A](2S)-2-cyano-3-(1H-indazol-5-yl)propanamide
C11 H10 N4 O
LSZLZUAHIJIGOY-QMMMGPOBSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1LB PDBBind:  4JG6 IC50: 360 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.28α = 90
b = 47.28β = 90
c = 291.97γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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