Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 43.19 kDa 
• Atom Count: 2463 
• Modelled Residue Count: 309 
• Deposited Residue Count: 382 
• Unique protein chains: 1

3WPN

Kinesin spindle protein Eg5 in complex with ATP-competitive inhibitor PVZB1194

• PDB DOI: 10.2210/pdb3WPN/pdb

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


• Deposited: 2014-01-14 Released: 2015-01-21 
• Deposition Author(s): Yokoyama, H., Katoh, S., Fujii, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.290 
• R-Value Work: 0.225 
• R-Value Observed: 0.231 

Literature

Structural basis of new allosteric inhibition in Kinesin spindle protein eg5

Yokoyama, H., Sawada, J., Katoh, S., Matsuno, K., Ogo, N., Ishikawa, Y., Hashimoto, H., Fujii, S., Asai, A.

(2015) ACS Chem Biol 10: 1128-1136

• PubMed: 25622007 
• DOI: 10.1021/cb500939x
• Primary Citation of Related Structures:  
  3WPN


• PubMed Abstract: 
  

Kinesin spindle protein Eg5 is a target for anticancer therapies, and small molecule inhibitors of its ATPase activity have been developed. We herein report for the first time the crystal structure of and biochemical studies on the Eg5 motor domain in complex with a new type of allosteric inhibitor. The biphenyl-type inhibitor PVZB1194 binds to the α4/α6 allosteric pocket 15 Å from the ATP-binding pocket, which differs from conventional allosteric inhibitors that bind to the allosteric L5/α2/α3 pocket of Eg5. Binding of the inhibitor is involved in the neck-linker conformation and also causes conformational changes around the ATP-binding pocket through Tyr104 to affect the interaction of ATP with the pocket. This structure provides useful information for the development of novel types of allosteric drugs as well as a novel insight into the molecular mechanism responsible for regulating the motor activity of kinesins.

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Organizational Affiliation: 

‡Center for Drug Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF11	A	382	Homo sapiens	Mutation(s): 0  Gene Names: EG5, KIF11, 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B4S	B [auth A]	3'-fluoro-4'-(trifluoromethyl)biphenyl-4-sulfonamide C13 H9 F4 N O2 S UEPKMFLFRNDVAW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B4S	BindingDB:  3WPN	IC50: 120 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.290 
• R-Value Work: 0.225 
• R-Value Observed: 0.231 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.912	α = 90
b = 95.425	β = 90
c = 59.015	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-14 
• Released Date: 2015-01-21 
Deposition Author(s): Yokoyama, H., Katoh, S., Fujii, S.

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Database references