1YRS

Crystal structure of KSP in complex with inhibitor 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Kinesin spindle protein (KSP) inhibitors. Part 1: The discovery of 3,5-diaryl-4,5-dihydropyrazoles as potent and selective inhibitors of the mitotic kinesin KSP

Cox, C.D.Breslin, M.J.Mariano, B.J.Coleman, P.J.Buser, C.A.Walsh, E.S.Hamilton, K.Huber, H.E.Kohl, N.E.Torrent, M.Yan, Y.Kuo, L.C.Hartman, G.D.

(2005) BIOORG.MED.CHEM.LETT. 15: 2041-2045

  • DOI: 10.1016/j.bmcl.2005.02.055

  • PubMed Abstract: 
  • Optimization of high-throughput screening (HTS) hits resulted in the discovery of 3,5-diaryl-4,5-dihydropyrazoles as potent and selective inhibitors of KSP. Dihydropyrazole 15 is a potent, cell-active KSP inhibitor that induces apoptosis and generate ...

    Optimization of high-throughput screening (HTS) hits resulted in the discovery of 3,5-diaryl-4,5-dihydropyrazoles as potent and selective inhibitors of KSP. Dihydropyrazole 15 is a potent, cell-active KSP inhibitor that induces apoptosis and generates aberrant mitotic spindles in human ovarian carcinoma cells at low nanomolar concentrations. X-ray crystallographic evidence is presented which demonstrates that these inhibitors bind in an allosteric pocket of KSP distant from the nucleotide and microtubule binding sites.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 4, Sumneytown Pike, West Point, PA 19486, USA. chris_cox@merck.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
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
L47
Query on L47

Download SDF File 
Download CCD File 
A, B
3-[(5S)-1-ACETYL-3-(2-CHLOROPHENYL)-4,5-DIHYDRO-1H-PYRAZOL-5-YL]PHENOL
C17 H15 Cl N2 O2
QBZAPFWYAPXRGQ-KRWDZBQOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L47IC50: 450 nM (100) BINDINGDB
L47IC50: 450 nM BINDINGMOAD
L47IC50: 450 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.300α = 90.00
b = 79.800β = 90.00
c = 159.600γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
SCALEPACKdata scaling
CNSphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance