2FL2

crystal structure of KSP in complex with inhibitor 19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.bmcl.2006.01.030
  • Primary Citation of Related Structures:  
    2FKY, 2FL2, 2FL6

  • 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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein KIF11
A, B
367Homo sapiensMutation(s): 0 
Gene Names: KIF11EG5KNSL1
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens)
Explore P52732 
Go to UniProtKB:  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
N4T
Query on N4T

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
(1S)-1-CYCLOPROPYL-2-[(2S)-4-(2,5-DIFLUOROPHENYL)-2-PHENYL-2,5-DIHYDRO-1H-PYRROL-1-YL]-2-OXOETHANAMINE
C21 H20 F2 N2 O
VCOUEHUEFUDZIS-PMACEKPBSA-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
N4T Binding MOAD:  2FL2 IC50: 2 (nM) from 1 assay(s)
BindingDB:  2FL2 IC50: 2 (nM) from 1 assay(s)
PDBBind:  2FL2 IC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.8α = 90
b = 79.5β = 90
c = 159γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations