4BXN

Eg5(WT) complex

• PDB DOI: https://doi.org/10.2210/pdb4BXN/pdb

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


• Deposited: 2013-07-15 Released: 2013-07-31 
• Deposition Author(s): Talapatra, S.K., Anthony, N.G., Mackay, S.P., Kozielski, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.274 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 

Literature

The Mitotic Kinesin Eg5 Overcomes Inhibition to the Phase I/II Clinical Candidate Sb743921 by an Allosteric Resistance Mechanism.

Talapatra, S.K., Anthony, N.G., Mackay, S.P., Kozielski, F.

(2013) J Med Chem 56: 6317

• PubMed: 23875972 
• DOI: https://doi.org/10.1021/jm4006274
• Primary Citation of Related Structures:  
  4A1Z, 4A28, 4AS7, 4B7B, 4BXN


• PubMed Abstract: 
  

  Development of drug resistance during cancer chemotherapy is one of the major causes of chemotherapeutic failure for the majority of clinical agents. The aim of this study was to investigate the underlying molecular mechanism of resistance developed by the mitotic kinesin Eg5 against the potent second-generation ispinesib analogue SB743921 (1), a phase I/II clinical candidate. Biochemical and biophysical data demonstrate that point mutations in the inhibitor-binding pocket decrease the efficacy of 1 by several 1000-fold. Surprisingly, the structures of wild-type and mutant Eg5 in complex with 1 display no apparent structural changes in the binding configuration of the drug candidate. Furthermore, ITC and modeling approaches reveal that resistance to 1 is not through conventional steric effects at the binding site but through reduced flexibility and changes in energy fluctuation pathways through the protein that influence its function. This is a phenomenon we have called "resistance by allostery".

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Organizational Affiliation: 

The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BS, Scotland, U.K. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 86.76 kDa 
• Atom Count: 5,521 
• Modelled Residue Count: 692 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6LX	DA [auth B], N [auth A]	N-(3-aminopropyl)-N-[(1R)-1-(3-benzyl-7-chloro-4-oxo-4H-chromen-2-yl)-2-methylpropyl]-4-methylbenzamide C31 H33 Cl N2 O3 PGXYIBJJCLWJST-MUUNZHRXSA-N
ADP	C [auth A], S [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CD	AA [auth B], BA [auth B], CA [auth B], D [auth A], E [auth A], EA [auth B], F [auth A], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], J [auth A], K [auth A], L [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL	FA [auth B], IA [auth B], JA [auth B], M [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
6LX	BindingDB:  4BXN	Ki: 0.5 (nM) from 1 assay(s)
		Kd: 10 (nM) from 1 assay(s)
		IC50: 0.14 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.274 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.426	α = 90
b = 81.426	β = 90
c = 115.202	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Talapatra, S.K., Anthony, N.G., Mackay, S.P., Kozielski, F.

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2014-09-17
  Changes: Atomic model, Derived calculations, Non-polymer description
• Version 1.3: 2019-11-20
  Changes: Advisory, Derived calculations, Other
• Version 1.4: 2023-03-08
  Changes: Advisory, Database references, Derived calculations
• Version 1.5: 2024-02-07
  Changes: Data collection, Refinement description