3CJO

Crystal structure of KSP in complex with inhibitor 30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Kinesin spindle protein (KSP) inhibitors. 9. Discovery of (2S)-4-(2,5-difluorophenyl)-n-[(3R,4S)-3-fluoro-1-methylpiperidin-4-yl]-2-(hydroxymethyl)-N-methyl-2-phenyl-2,5-dihydro-1H-pyrrole-1-carboxamide (MK-0731) for the treatment of taxane-refractory cancer.

Cox, C.D.Coleman, P.J.Breslin, M.J.Whitman, D.B.Garbaccio, R.M.Fraley, M.E.Buser, C.A.Walsh, E.S.Hamilton, K.Schaber, M.D.Lobell, R.B.Tao, W.Davide, J.P.Diehl, R.E.Abrams, M.T.South, V.J.Huber, H.E.Torrent, M.Prueksaritanont, T.Li, C.Slaughter, D.E.Mahan, E.Fernandez-Metzler, C.Yan, Y.Kuo, L.C.Kohl, N.E.Hartman, G.D.

(2008) J.Med.Chem. 51: 4239-4252

  • DOI: 10.1021/jm800386y

  • PubMed Abstract: 
  • Inhibition of kinesin spindle protein (KSP) is a novel mechanism for treatment of cancer with the potential to overcome limitations associated with currently employed cytotoxic agents. Herein, we describe a C2-hydroxymethyl dihydropyrrole KSP inhibit ...

    Inhibition of kinesin spindle protein (KSP) is a novel mechanism for treatment of cancer with the potential to overcome limitations associated with currently employed cytotoxic agents. Herein, we describe a C2-hydroxymethyl dihydropyrrole KSP inhibitor ( 11) that circumvents hERG channel binding and poor in vivo potency, issues that limited earlier compounds from our program. However, introduction of the C2-hydroxymethyl group caused 11 to be a substrate for cellular efflux by P-glycoprotein (Pgp). Utilizing knowledge garnered from previous KSP inhibitors, we found that beta-fluorination modulated the p K a of the piperidine nitrogen and reduced Pgp efflux, but the resulting compound ( 14) generated a toxic metabolite in vivo. Incorporation of fluorine in a strategic, metabolically benign position by synthesis of an N-methyl-3-fluoro-4-(aminomethyl)piperidine urea led to compound 30 that has an optimal in vitro and metabolic profile. Compound 30 (MK-0731) was recently studied in a phase I clinical trial in patients with taxane-refractory solid tumors.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, P.O. Box 4, Sumneytown Pike, West Point, Pennsylvania 19486, USA. chris_cox@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kinesin-like protein KIF11
A, B
367Homo 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
K30
Query on K30

Download SDF File 
Download CCD File 
A, B
(2S)-4-(2,5-difluorophenyl)-N-[(3R,4S)-3-fluoro-1-methylpiperidin-4-yl]-2-(hydroxymethyl)-N-methyl-2-phenyl-2,5-dihydro-1H-pyrrole-1-carboxamide
C25 H28 F3 N3 O2
MYBGWENAVMIGMM-GIFXNVAJSA-N
 Ligand Interaction
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K30IC50: 2.2 nM BINDINGMOAD
K30IC50: 2.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.758α = 90.00
b = 79.374β = 90.00
c = 158.853γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSphasing
CrystalCleardata collection
HKL-2000data reduction
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-03-13 
  • Released Date: 2008-07-01 
  • Deposition Author(s): Yan, Y.

Revision History 

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