2Q2Y

Crystal Structure of KSP in complex with Inhibitor 1

• PDB DOI: https://doi.org/10.2210/pdb2Q2Y/pdb

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


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

---

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 

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

• PubMed: 17766111 
• DOI: https://doi.org/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.

---

Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 4, Sumneytown Pike, 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: 83.71 kDa 
• Atom Count: 5,559 
• 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, TRIP5
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
MKR	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
ADP	D [auth A], G [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MKR	PDBBind:  2Q2Y	IC50: 1.6 (nM) from 1 assay(s)
	BindingDB:  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 = 68.86	α = 90
b = 79.8	β = 90
c = 159.57	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2007-09-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations