2PG2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: 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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein KIF11
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
GTEx:  ENSG00000138160 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52732
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
K01
Query on K01

Download Ideal Coordinates CCD File 
E [auth A],
H [auth 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
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
K01 PDBBind:  2PG2 IC50: 1700 (nM) from 1 assay(s)
BindingDB:  2PG2 IC50: 1700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.064α = 90
b = 80.35β = 96.83
c = 69.313γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description