2FKY

crystal structure of KSP in complex with inhibitor 13

• PDB DOI: https://doi.org/10.2210/pdb2FKY/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-05 Released: 2006-02-07 
• Deposition Author(s): Yan, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.273 
• R-Value Work: 0.235 
• R-Value Observed: 0.240 

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

• PubMed: 16439123 
• 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83.55 kDa 
• Atom Count: 5,523 
• Modelled Residue Count: 660 
• Deposited Residue Count: 734 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF11	A, B	367	Homo sapiens	Mutation(s): 0  Gene Names: KIF11, EG5, KNSL1
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens) Explore P52732  Go to UniProtKB:  P52732
PHAROS:  P52732 GTEx:  ENSG00000138160

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], G [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
N2T	E [auth A], H [auth B]	(2S)-4-(2,5-DIFLUOROPHENYL)-N-METHYL-2-PHENYL-N-PIPERIDIN-4-YL-2,5-DIHYDRO-1H-PYRROLE-1-CARBOXAMIDE C23 H25 F2 N3 O NKLVBHMAIMEVEH-QFIPXVFZSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
N2T	PDBBind:  2FKY	IC50: 2.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.273 
• R-Value Work: 0.235 
• R-Value Observed: 0.240 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.2	α = 90
b = 79.6	β = 90
c = 159	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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