3FZ1

Crystal structure of a benzthiophene inhibitor bound to human Cyclin-dependent Kinase-2 (CDK-2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.bmcl.2009.02.017
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell division protein kinase 2
A
298Homo sapiensMutation(s): 0 
Gene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B98
Query on B98

Download SDF File 
Download CCD File 
A
(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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B98IC50: 12 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.717α = 90.00
b = 71.709β = 90.00
c = 72.242γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description