2FL6

crystal structure of KSP in complex with inhibitor 6

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Kinesin spindle protein (KSP) inhibitors. Part 2: the design, synthesis, and characterization of 2,4-diaryl-2,5-dihydropyrrole inhibitors of the mitotic kinesin KSP.

Fraley, M.E., Garbaccio, R.M., Arrington, K.L., Hoffman, W.F., Tasber, E.S., Coleman, P.J., Buser, C.A., Walsh, E.S., Hamilton, K., Fernandes, C., Schaber, M.D., Lobell, R.B., Tao, W., South, V.J., Yan, Y., Kuo, L.C., Prueksaritanont, T., Shu, C., Torrent, M., Heimbrook, D.C., Kohl, N.E., Huber, H.E., Hartman, G.D.

(2006) Bioorg Med Chem Lett 16: 1775-1779

  • DOI: 10.1016/j.bmcl.2006.01.030
  • Primary Citation of Related Structures:  
    2FL6, 2FL2, 2FKY

  • PubMed Abstract: 

    • The evolution of 2,4-diaryl-2,5-dihydropyrroles as inhibitors of KSP is described. Introduction of basic amide and urea moieties to the dihydropyrrole nucleus enhanced potency and aqueous solubility, simultaneously, and provided compounds that caused ...

    The evolution of 2,4-diaryl-2,5-dihydropyrroles as inhibitors of KSP is described. Introduction of basic amide and urea moieties to the dihydropyrrole nucleus enhanced potency and aqueous solubility, simultaneously, and provided compounds that caused mitotic arrest of A2780 human ovarian carcinoma cells with EC(50)s<10nM. Ancillary hERG activity was evaluated for this series of inhibitors.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA. mark_fraley@merck.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-like protein KIF11A, B367Homo sapiensMutation(s): 0 
Gene Names: KIF11, EG5, KNSL1, TRIP5
Find proteins for P52732 (Homo sapiens)
Explore P52732 
Go to UniProtKB:  P52732
NIH Common Fund Data Resources
PHAROS  P52732
GTEx  ENSG00000138160
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
N5T
Query on N5T
Download CCD File 
A, B
(2S)-4-(2,5-DIFLUOROPHENYL)-N,N-DIMETHYL-2-PHENYL-2,5-DIHYDRO-1H-PYRROLE-1-CARBOXAMIDE
C19 H18 F2 N2 O
WFFMEXQHWXEKBV-SFHVURJKSA-N		 Ligand Interaction
MG
Query on MG
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N5TIC50 :  38   nM  PDBBind
N5TIC50:  38   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.9α = 90
b = 79.4β = 90
c = 158.8γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2006-01-05 
  • Released Date: 2006-02-07 
    • Deposition Author(s): Yan, Y.

Revision History 

  • Version 1.0: 2006-02-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance