3FYK

Crystal structure of a benzthiophene lead bound to MAPKAP Kinase-2 (MK-2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.296 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.265 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

Starting Models: experimental
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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 B98Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Benzothiophene inhibitors of MK2. Part 2: improvements in kinase selectivity and cell potency.

Anderson, D.R.Meyers, M.J.Kurumbail, R.G.Caspers, N.Poda, G.I.Long, S.A.Pierce, B.S.Mahoney, M.W.Mourey, R.J.Parikh, M.D.

(2009) Bioorg Med Chem Lett 19: 4882-4884

  • DOI: https://doi.org/10.1016/j.bmcl.2009.02.017
  • Primary Citation of Related Structures:  
    3FYJ, 3FYK, 3FZ1

  • PubMed Abstract: 

    Optimization of kinase selectivity for a set of benzothiophene MK2 inhibitors provided analogs with potencies of less than 500 nM in a cell based assay. The selectivity of the inhibitors can be rationalized by examination of X-ray crystal structures of inhibitors bound to MK2.


  • Organizational Affiliation

    Pfizer Global Research and Development, St Louis Laboratories, Chesterfield, MO 63017, USA. david.r.anderson@pfizer.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 2A [auth X]327Homo sapiensMutation(s): 0 
Gene Names: MAPKAP-2MAPKAPK2
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B98
Query on B98

Download Ideal Coordinates CCD File 
B [auth X](3R)-3-(aminomethyl)-9-methoxy-1,2,3,4-tetrahydro-5H-[1]benzothieno[3,2-e][1,4]diazepin-5-one
C13 H15 N3 O2 S
TXYKBKYDFZQOCB-SSDOTTSWSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
B98 BindingDB:  3FYK IC50: min: 5, max: 2600 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.296 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.265 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 254.598α = 90
b = 254.598β = 90
c = 254.598γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
AMoREphasing

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 B98Click on this verticalbar to view details

Entry History 

Deposition Data

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: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description