Crystal Structure of a Squarate Inhibitor bound to MAPKAP Kinase-2

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.284 

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Identification and SAR of squarate inhibitors of mitogen activated protein kinase-activated protein kinase 2 (MK-2)

Lovering, F.Kirincich, S.Wang, W.Combs, K.Resnick, L.Sabalski, J.E.Butera, J.Liu, J.Parris, K.Telliez, J.B.

(2009) Bioorg Med Chem 17: 3342-3351

  • DOI: https://doi.org/10.1016/j.bmc.2009.03.041
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A novel series of inhibitors for mitogen activated protein kinase-activated protein kinase 2 (MK-2) are reported. These squarate based inhibitors were identified via a high-throughput screen. An MK2 co-structure with the starting ligand was obtained and a structure based approach was followed to optimize potency and selectivity.

  • Organizational Affiliation

    Chemical Sciences, Wyeth Research, Cambridge, MA 02140, USA. flovering@wyeth.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 2325Homo sapiensMutation(s): 0 
Gene Names: MAPKAPK2
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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 793

Download Ideal Coordinates CCD File 
B [auth A]3-{[(1R)-1-phenylethyl]amino}-4-(pyridin-4-ylamino)cyclobut-3-ene-1,2-dione
C17 H15 N3 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
793 PDBBind:  3FPM IC50: 8900 (nM) from 1 assay(s)
BindingDB:  3FPM IC50: 8900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.284 
  • Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 254.658α = 90
b = 254.658β = 90
c = 254.658γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2009-04-07 
  • Deposition Author(s): Parris, K.D.

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description