2UYI

Crystal structure of KSP in complex with ADP and thiophene containing inhibitor 33

• PDB DOI: https://doi.org/10.2210/pdb2UYI/pdb

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


• Deposited: 2007-04-07 Released: 2007-05-22 
• Deposition Author(s): Lee, T.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.294 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 

Literature

Synthesis and Sar of Thiophene Containing Kinesin Spindle Protein (Ksp) Inhibitors.

Pinkerton, A.B., Lee, T.T., Hoffman, T.Z., Wang, Y., Kahraman, M., Cook, T.G., Severance, D., Gahman, T.C., Noble, S.A., Shiau, A.K., Davis, R.L.

(2007) Bioorg Med Chem Lett 17: 3562

• PubMed: 17498954 
• DOI: https://doi.org/10.1016/j.bmcl.2007.04.076
• Primary Citation of Related Structures:  
  2PG2, 2UYI, 2UYM


• PubMed Abstract: 
  

  We have identified and synthesized a series of thiophene containing inhibitors of kinesin spindle protein. SAR studies led to the synthesis of 33, which was co-crystallized with KSP and determined to bind to an allosteric pocket previously described for other known KSP inhibitors.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Kalypsys, Inc., 10420 Wateridge Circle, San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 83.77 kDa 
• Atom Count: 5,580 
• Modelled Residue Count: 662 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KINESIN-LIKE PROTEIN KIF11	A, B	368	Homo sapiens	Mutation(s): 0
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	C [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
K02	E [auth A], H [auth B]	(5R)-N,N-DIETHYL-5-METHYL-2-[(THIOPHEN-2-YLCARBONYL)AMINO]-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-3-CARBOXAMIDE C19 H24 N2 O2 S2 UQKSYQYWUHUIEH-GFCCVEGCSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
K02	BindingDB:  2UYI	IC50: 480 (nM) from 1 assay(s)
	PDBBind:  2UYI	IC50: 480 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.294 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.535	α = 90
b = 80.139	β = 90
c = 159.036	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Lee, T.T.

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other