3L9H

X-ray structure of mitotic kinesin-5 (KSP, KIF11, Eg5)in complex with the hexahydro-2H-pyrano[3,2-c]quinoline EMD 534085


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The discovery and optimization of hexahydro-2H-pyrano[3,2-c]quinolines (HHPQs) as potent and selective inhibitors of the mitotic kinesin-5.

Schiemann, K.Finsinger, D.Zenke, F.Amendt, C.Knochel, T.Bruge, D.Buchstaller, H.P.Emde, U.Stahle, W.Anzali, S.

(2010) Bioorg Med Chem Lett 20: 1491-1495

  • DOI: 10.1016/j.bmcl.2010.01.110
  • Primary Citation of Related Structures:  
    3L9H

  • PubMed Abstract: 
  • Here we describe the discovery and optimization of hexahydro-2H-pyrano[3,2-c]quinolines (HHPQs) as potent and selective inhibitors of the mitotic kinesin-5 originally found during a high-throughput screening (HTS) campaign sampling our in-house compound collection ...

    Here we describe the discovery and optimization of hexahydro-2H-pyrano[3,2-c]quinolines (HHPQs) as potent and selective inhibitors of the mitotic kinesin-5 originally found during a high-throughput screening (HTS) campaign sampling our in-house compound collection. The compounds optimized subsequently and characterized herein were potently inhibiting the ATPase activity of Kinesin-5 and also exhibited consistent cellular activity, in that cells arrested in mitosis and apoptosis induction could be observed. X-ray crystallographic data demonstrated that these inhibitors bind in an allosteric pocket of Kinesin-5 distant from the nucleotide and microtubule binding sites. The selected clinical candidate EMD 534085 caused strong growth inhibition in human tumor xenograft models using Colo 205 colon carcinoma cells at doses below 30mg/kg administered twice weekly without showing severe toxicity as determined by loss of body weight.


    Organizational Affiliation

    MS-RTC-MedChem DA35, Merck Serono, Merck KGaA, Frankfurter Strasse 250, D-64293 Darmstadt, Germany. kai.schiemann@merck.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-like protein KIF11A, B368Homo sapiensMutation(s): 0 
Gene Names: EG5KIF11KNSL1TRIP5
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens)
Explore P52732 
Go to UniProtKB:  P52732
PHAROS:  P52732
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52732
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EMQ
Query on EMQ

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
1-[2-(dimethylamino)ethyl]-3-{[(2R,4aS,5R,10bS)-5-phenyl-9-(trifluoromethyl)-3,4,4a,5,6,10b-hexahydro-2H-pyrano[3,2-c]quinolin-2-yl]methyl}urea
C25 H31 F3 N4 O2
MARIUIDCPUZLKZ-FUKQBSRTSA-N
 Ligand Interaction
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EMQ Binding MOAD:  3L9H IC50: 8 (nM) from 1 assay(s)
BindingDB:  3L9H IC50: 8 (nM) from 1 assay(s)
PDBBind:  3L9H IC50: 8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.95α = 90
b = 79.718β = 96.88
c = 69.513γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2010-01-05 
  • Released Date: 2010-03-02 
  • Deposition Author(s): Knoechel, T.

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance