3KC3

MK2 complexed to inhibitor N4-(7-(benzofuran-2-yl)-1H-indazol-5-yl)pyrimidine-2,4-diamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

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 MK2Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

2,4-Diaminopyrimidine MK2 inhibitors. Part I: Observation of an unexpected inhibitor binding mode.

Argiriadi, M.A.Ericsson, A.M.Harris, C.M.Banach, D.L.Borhani, D.W.Calderwood, D.J.Demers, M.D.Dimauro, J.Dixon, R.W.Hardman, J.Kwak, S.Li, B.Mankovich, J.A.Marcotte, D.Mullen, K.D.Ni, B.Pietras, M.Sadhukhan, R.Sousa, S.Tomlinson, M.J.Wang, L.Xiang, T.Talanian, R.V.

(2010) Bioorg Med Chem Lett 20: 330-333

  • DOI: https://doi.org/10.1016/j.bmcl.2009.10.102
  • Primary Citation of Related Structures:  
    3KA0, 3KC3

  • PubMed Abstract: 

    MK2 is a Ser/Thr kinase of significant interest as an anti-inflammatory drug discovery target. Here we describe the development of in vitro tools for the identification and characterization of MK2 inhibitors, including validation of inhibitor interactions with the crystallography construct and determination of the unique binding mode of 2,4-diaminopyrimidine inhibitors in the MK2 active site. Use of these tools in the optimization of a potent and selective inhibitor lead series is described in the accompanying Letter.


  • Organizational Affiliation

    Abbott Laboratories, 100 Research Drive, Worcester, MA 01605-5314, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 2
A, B, C, D, E
324Homo 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
MK2
Query on MK2

Download Ideal Coordinates CCD File 
M [auth A]
N [auth B]
O [auth C]
P [auth D]
Q [auth E]
N~4~-[7-(1-benzofuran-2-yl)-1H-indazol-5-yl]pyrimidine-2,4-diamine
C19 H14 N6 O
IQDDLNJTLVXFQA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MK2 PDBBind:  3KC3 IC50: 160 (nM) from 1 assay(s)
BindingDB:  3KC3 IC50: 1300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.351α = 90
b = 179.793β = 90
c = 214.376γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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 MK2Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations