3KGA | pdb_00003kga

Crystal structure of MAPKAP kinase 2 (MK2) complexed with a potent 3-aminopyrazole ATP site inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3KGA/pdb

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


• Deposited: 2009-10-28 Released: 2010-01-26 
• Deposition Author(s): Kroemer, M., Velcicky, J., Izaac, A., Be, C., Huppertz, C., Pflieger, D., Schlapbach, A., Scheufler, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Novel 3-aminopyrazole inhibitors of MK-2 discovered by scaffold hopping strategy.

Velcicky, J., Feifel, R., Hawtin, S., Heng, R., Huppertz, C., Koch, G., Kroemer, M., Moebitz, H., Revesz, L., Scheufler, C., Schlapbach, A.

(2010) Bioorg Med Chem Lett 20: 1293-1297

• PubMed: 20060294 
• DOI: https://doi.org/10.1016/j.bmcl.2009.10.138
• Primary Citation Related Structures: 
  3KGA


• PubMed Abstract: 
  

  New, selective 3-aminopyrazole based MK2-inhibitors were discovered by scaffold hopping strategy. The new derivatives proved to inhibit intracellular phosphorylation of hsp27 as well as LPS-induced TNFalpha release in cells. In addition, selected derivative 14e also inhibited LPS-induced TNFalpha release in vivo.

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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: 35.01 kDa 
• Atom Count: 2,466 
• Modeled 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
LX9	C [auth A]	6-{3-amino-1-[3-(1H-indol-6-yl)phenyl]-1H-pyrazol-4-yl}-3,4-dihydroisoquinolin-1(2H)-one C26 H21 N5 O ZTKOUSVWVUFWQC-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LX9	BindingDB:  3KGA	IC50: 61 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.12	α = 90
b = 103.12	β = 90
c = 165.415	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Kroemer, M., Velcicky, J., Izaac, A., Be, C., Huppertz, C., Pflieger, D., Schlapbach, A., Scheufler, C.

Revision History  

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection