2PG2

Crystal structure of KSP in complex with ADP and thiophene containing inhibitor 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.849 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 3562-3569

  • DOI: 10.1016/j.bmcl.2007.04.076
  • Primary Citation of Related Structures:  

  • 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 ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kinesin-like protein KIF11
A, B
368Homo sapiensMutation(s): 0 
Gene Names: KIF11 (EG5, KNSL1, TRIP5)
Find proteins for P52732 (Homo sapiens)
Go to Gene View: KIF11
Go to UniProtKB:  P52732
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
K01
Query on K01

Download SDF File 
Download CCD File 
A, B
N,N-DIETHYL-2-[(2-THIENYLCARBONYL)AMINO]-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-3-CARBOXAMIDE
C18 H22 N2 O2 S2
NZTHBWHANVWSRX-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K01IC50: 1700 nM (100) BINDINGDB
K01IC50: 1700 nM BINDINGMOAD
K01IC50: 1700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.849 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 161.064α = 90.00
b = 80.350β = 96.83
c = 69.313γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-04-06 
  • Released Date: 2007-06-05 
  • Deposition Author(s): Lee, T.T.

Revision History 

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance