3SHE

Novel ATP-competitive MK2 inhibitors with potent biochemical and cell-based activity throughout the series


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Novel ATP competitive MK2 inhibitors with potent biochemical and cell-based activity throughout the series.

Oubrie, A.Kaptein, A.de Zwart, E.Hoogenboom, N.Goorden, R.van de Kar, B.van Hoek, M.de Kimpe, V.van der Heijden, R.Borsboom, J.Kazemier, B.de Roos, J.Scheffers, M.Lommerse, J.Schultz-Fademrecht, C.Barf, T.

(2012) Bioorg Med Chem Lett 22: 613-618

  • DOI: https://doi.org/10.1016/j.bmcl.2011.10.071
  • Primary Citation of Related Structures:  
    3SHE

  • PubMed Abstract: 

    Optimization of our previously described pyrrolopiperidone series led to the identification of a new benzamide sub-series, which exhibits consistently high potency in biochemical and cell-based assays throughout the series. Strong inhibition of LPS-induced production of the cytokine TNFα is coupled to the regulation of HSP27 phosphorylation, indicating that the observed cellular effects result from the inhibition of MK2. X-ray crystallographic and computational analyses provide a rationale for the high potency of the series.


  • Organizational Affiliation

    Merck Research Laboratories, MSD, PO Box 20, 5340 BH Oss, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 3317Homo sapiensMutation(s): 0 
Gene Names: MAPKAPK3
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16644 (Homo sapiens)
Explore Q16644 
Go to UniProtKB:  Q16644
PHAROS:  Q16644
GTEx:  ENSG00000114738 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16644
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I85
Query on I85

Download Ideal Coordinates CCD File 
B [auth A]N-{4-[(3S)-4'-oxo-1',4',5',6'-tetrahydrospiro[piperidine-3,7'-pyrrolo[3,2-c]pyridin]-2'-yl]pyridin-2-yl}-3-(trifluoromethyl)benzamide
C24 H22 F3 N5 O2
FEVPBNYNYKIJAR-QHCPKHFHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.946α = 90
b = 76.026β = 106.68
c = 60.288γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-01-11
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations