3M2W

Crystal structure of MAPKAK kinase 2 (MK2) complexed with a spiroazetidine-tetracyclic ATP site inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

In vivo and in vitro SAR of tetracyclic MAPKAP-K2 (MK2) inhibitors. Part II.

Revesz, L.Schlapbach, A.Aichholz, R.Dawson, J.Feifel, R.Hawtin, S.Littlewood-Evans, A.Koch, G.Kroemer, M.Mobitz, H.Scheufler, C.Velcicky, J.Huppertz, C.

(2010) Bioorg Med Chem Lett 20: 4719-4723

  • DOI: https://doi.org/10.1016/j.bmcl.2010.04.023
  • Primary Citation of Related Structures:  
    3M2W

  • PubMed Abstract: 

    Spirocyclopropane- and spiroazetidine-substituted tetracycles 13D-E and 16A are described as orally active MK2 inhibitors. The spiroazetidine derivatives are potent MK2 inhibitors with IC(50)<3 nM and inhibit the release of TNFalpha (IC(50)<0.3 microM) from hPBMCs and hsp27 phosphorylation in anisomycin stimulated THP-1 cells. The spirocyclopropane analogues are less potent against MK2 (IC(50)=0.05-0.23 microM), less potent in cells (IC(50)<1.1 microM), but show good oral absorption. Compound 13E (100mg/kg po; bid) showed oral activity in rAIA and mCIA, with significant reduction of swelling and histological score.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. laszlo.revesz@pharma.novartis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 2299Homo sapiensMutation(s): 1 
Gene Names: MAPKAPK2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49137 (Homo sapiens)
Explore P49137 
Go to UniProtKB:  P49137
PHAROS:  P49137
GTEx:  ENSG00000162889 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49137
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L8I
Query on L8I

Download Ideal Coordinates CCD File 
B [auth A]2'-(2-fluorophenyl)-1-methyl-6',8',9',11'-tetrahydrospiro[azetidine-3,10'-pyrido[3',4':4,5]pyrrolo[2,3-f]isoquinolin]-7'(5'H)-one
C23 H21 F N4 O
XZZOJFOFCDHYRX-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
L8I PDBBind:  3M2W IC50: 3 (nM) from 1 assay(s)
BindingDB:  3M2W IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.982α = 90
b = 102.982β = 90
c = 165.433γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-06
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-02-21
    Changes: Data collection