3M2W

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

• PDB DOI: https://doi.org/10.2210/pdb3M2W/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-03-08 Released: 2010-07-28 
• Deposition Author(s): Kroemer, M., Revesz, L., Be, C., Izaac, A., Huppertz, C., Schlapbach, A., Scheufler, C.

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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 

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

• PubMed: 20591669 
• 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.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.98 kDa 
• Atom Count: 2,529 
• Modelled Residue Count: 290 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAP kinase-activated protein kinase 2	A	299	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L8I	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	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 102.982	α = 90
b = 102.982	β = 90
c = 165.433	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Kroemer, M., Revesz, L., Be, C., Izaac, A., Huppertz, C., Schlapbach, A., Scheufler, C.

Revision History  

• 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