3R30 | pdb_00003r30

MK2 kinase bound to Compound 2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.332 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.279 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.284 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CD2Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    Merck Research Laboratories, MSD, Oss, The Netherlands.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 2319Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49137
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD2
Query on CD2
Download Ideal Coordinates CCD File 
B [auth A]1-(2-aminoethyl)-3-[2-(quinolin-3-yl)pyridin-4-yl]-1H-pyrazole-5-carboxylic acid
C20 H17 N5 O2
IDPLDWUOSVSMNS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CD2 BindingDB:  3R30 EC50: 28 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.332 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.279 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.284 (Depositor) 
Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 253.297α = 90
b = 253.297β = 90
c = 253.297γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CD2Click on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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