2Q2Y

Crystal Structure of KSP in complex with Inhibitor 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Kinesin spindle protein (KSP) inhibitors. Part 8: Design and synthesis of 1,4-diaryl-4,5-dihydropyrazoles as potent inhibitors of the mitotic kinesin KSP.

Roecker, A.J.Coleman, P.J.Mercer, S.P.Schreier, J.D.Buser, C.A.Walsh, E.S.Hamilton, K.Lobell, R.B.Tao, W.Diehl, R.E.South, V.J.Davide, J.P.Kohl, N.E.Yan, Y.Kuo, L.C.Li, C.Fernandez-Metzler, C.Mahan, E.A.Prueksaritanont, T.Hartman, G.D.

(2007) Bioorg Med Chem Lett 17: 5677-5682

  • DOI: 10.1016/j.bmcl.2007.07.074
  • Primary Citation of Related Structures:  
    2Q2Y, 2Q2Z

  • PubMed Abstract: 
  • Inspired by previous efforts in the pyrazolobenzoxazine class of KSP inhibitors, the design and synthesis of 1,4-diaryl-4,5-dihydropyrazole inhibitors of KSP are described. Crystallographic evidence of binding mode and in vivo potency data is also highlighted ...

    Inspired by previous efforts in the pyrazolobenzoxazine class of KSP inhibitors, the design and synthesis of 1,4-diaryl-4,5-dihydropyrazole inhibitors of KSP are described. Crystallographic evidence of binding mode and in vivo potency data is also highlighted.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 4, Sumneytown Pike, West Point, PA 19486, USA. anthony_roecker@merck.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-like protein KIF11A, B367Homo sapiensMutation(s): 0 
Gene Names: KIF11EG5KNSL1TRIP5
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MKR
Query on MKR

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
1-{(3R,3AR)-3-[3-(4-ACETYLPIPERAZIN-1-YL)PROPYL]-8-FLUORO-3-PHENYL-3A,4-DIHYDRO-3H-PYRAZOLO[5,1-C][1,4]BENZOXAZIN-2-YL}ETHANONE
C27 H31 F N4 O3
BWKAHABETZLDBG-AHKZPQOWSA-N
 Ligand Interaction
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
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MKR PDBBind:  2Q2Y IC50: 1.6 (nM) from 1 assay(s)
BindingDB:  2Q2Y IC50: 1.6 (nM) from 1 assay(s)
Binding MOAD:  2Q2Y IC50: 1.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.86α = 90
b = 79.8β = 90
c = 159.57γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2007-05-29 
  • Released Date: 2007-09-18 
  • Deposition Author(s): Yan, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance