3R2Y

MK2 kinase bound to Compound 1


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 2A319Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49137
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P4O
Query on P4O

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
MLI
Query on MLI

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 253.258α = 90
b = 253.258β = 90
c = 253.258γ = 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 



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