3R2Y

MK2 kinase bound to Compound 1

• PDB DOI: https://doi.org/10.2210/pdb3R2Y/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-03-15 Released: 2011-05-25 
• Deposition Author(s): Oubrie, A., Leonard, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.334 
• R-Value Work: 0.289 
• R-Value Observed: 0.294 

Literature

Structure-based lead identification of ATP-competitive MK2 inhibitors.

Barf, T., Kaptein, A., Wilde, S., Heijden, R., Someren, R., Demont, D., Schultz-Fademrecht, C., Versteegh, J., Zeeland, M., Seegers, N., Kazemier, B., Kar, B., Hoek, M., Roos, J., Klop, H., Smeets, R., Hofstra, C., Hornberg, J., Oubrie, A.

(2011) Bioorg Med Chem Lett 21: 3818-3822

• PubMed: 21565500 
• DOI: https://doi.org/10.1016/j.bmcl.2011.04.018
• Primary Citation of Related Structures:  
  3R1N, 3R2B, 3R2Y, 3R30


• PubMed Abstract: 
  

  MK2 kinase is a promising drug discovery target for the treatment of inflammatory diseases. Here, we describe the discovery of novel MK2 inhibitors using X-ray crystallography and structure-based drug design. The lead has in vivo efficacy in a short-term preclinical model.

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Organizational Affiliation: 

Merck Research Laboratories, MSD, Oss, The Netherlands.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.44 kDa 
• Atom Count: 2,100 
• Modelled Residue Count: 259 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAP kinase-activated protein kinase 2	A	319	Homo sapiens	Mutation(s): 0  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
P4O	D [auth A]	2-(2-QUINOLIN-3-YLPYRIDIN-4-YL)-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE C21 H16 N4 O OWFLADWRSCINST-UHFFFAOYSA-N
MLI	B [auth A], C [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
P4O	PDBBind:  3R2Y	IC50: 8.5 (nM) from 1 assay(s)
	BindingDB:  3R2Y	IC50: 8.5 (nM) from 1 assay(s)
		EC50: 49 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.334 
• R-Value Work: 0.289 
• R-Value Observed: 0.294 
• Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 253.258	α = 90
b = 253.258	β = 90
c = 253.258	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Oubrie, A., Leonard, P.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations