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

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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This is version 1.3 of the entry. See complete history


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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein kinase 2298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDK2_Human
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B98

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
B98 PDBBind:  3FZ1 IC50: 12 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.717α = 90
b = 71.709β = 90
c = 72.242γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

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