Crystal structure of KSP in complex with ADP and thiophene containing inhibitor 37

Experimental Data Snapshot

  • Resolution: 2.11 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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Synthesis and Sar of Thiophene Containing Kinesin Spindle Protein (Ksp) Inhibitors.

Pinkerton, A.B.Lee, T.T.Hoffman, T.Z.Wang, Y.Kahraman, M.Cook, T.G.Severance, D.Gahman, T.C.Noble, S.A.Shiau, A.K.Davis, R.L.

(2007) Bioorg Med Chem Lett 17: 3562

  • DOI: https://doi.org/10.1016/j.bmcl.2007.04.076
  • Primary Citation of Related Structures:  
    2PG2, 2UYI, 2UYM

  • PubMed Abstract: 

    We have identified and synthesized a series of thiophene containing inhibitors of kinesin spindle protein. SAR studies led to the synthesis of 33, which was co-crystallized with KSP and determined to bind to an allosteric pocket previously described for other known KSP inhibitors.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Kalypsys, Inc., 10420 Wateridge Circle, San Diego, CA 92121, USA. apinkerton@kalypsys.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
368Homo sapiensMutation(s): 0 
Gene Names: KIF11EG5KNSL1TRIP5
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens)
Explore P52732 
Go to UniProtKB:  P52732
PHAROS:  P52732
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52732
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
K03 PDBBind:  2UYM IC50: 3100 (nM) from 1 assay(s)
Binding MOAD:  2UYM IC50: 3100 (nM) from 1 assay(s)
BindingDB:  2UYM IC50: 3100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.11 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.79α = 90
b = 80.452β = 96.16
c = 68.831γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2007-05-22 
  • Deposition Author(s): Lee, T.T.

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance