6HKY

Eg5-inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Is the Fate of Clinical Candidate Arry-520 Already Sealed? Predicting Resistance in Eg5-Inhibitor Complexes.

Indorato, R.L.Talapatra, S.K.Lin, F.Haider, S.Mackay, S.P.Kozielski, F.Skoufias, D.A.

(2019) Mol Cancer Ther 18: 2394-2406

  • DOI: 10.1158/1535-7163.MCT-19-0154
  • Primary Citation of Related Structures:  
    6HKX, 6HKY

  • PubMed Abstract: 
  • Arry-520 is an advanced drug candidate from the Eg5 inhibitor class undergoing clinical evaluation in patients with relapsed or refractory multiple myeloma. Here, we show by structural analysis that Arry-520 binds stoichiometrically to the motor domain of Eg5 in the conventional allosteric loop L5 pocket in a complex that suggests the same structural mechanism as other Eg5 inhibitors ...

    Arry-520 is an advanced drug candidate from the Eg5 inhibitor class undergoing clinical evaluation in patients with relapsed or refractory multiple myeloma. Here, we show by structural analysis that Arry-520 binds stoichiometrically to the motor domain of Eg5 in the conventional allosteric loop L5 pocket in a complex that suggests the same structural mechanism as other Eg5 inhibitors. We have previously shown that acquired resistance through mutations in the allosteric-binding site located at loop L5 in the Eg5 structure appears to be independent of the inhibitors' scaffold, which suggests that Arry-520 will ultimately have the same fate. When Arry-520 was assessed in two cell lines selected for the expression of either Eg5(D130A) or Eg5(L214A) STLC-resistant alleles, mutations previously shown to convey resistance to this class of inhibitors, it was inactive in both. Surprisingly, when the cells were challenged with ispinesib, another Eg5 inhibitor, the Eg5(D130A) cells were resistant, but those expressing Eg5(L214A) were strikingly sensitive. Molecular dynamics simulations suggest that subtle differences in ligand binding and flexibility in both compound and protein may alter allosteric transmission from the loop L5 site that do not necessarily result in reduced inhibitory activity in mutated Eg5 structures. Although we predict that cells challenged with Arry-520 in the clinical setting are likely to acquire resistance through point mutations in the Eg5-binding site, the data for ispinesib suggest that this resistance mechanism is not scaffold independent as previously thought, and new inhibitors can be designed that retain inhibitory activity in these resistant cells.


    Organizational Affiliation

    Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France. dimitrios.skoufias@ibs.fr f.kozielski@ucl.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-like protein KIF11A, B, C368Homo sapiensMutation(s): 0 
Gene Names: KIF11EG5KNSL1TRIP5
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens)
Explore P52732 
Go to UniProtKB:  P52732
PHAROS:  P52732
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
D [auth A], G [auth B], J [auth C]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
GCE (Subject of Investigation/LOI)
Query on GCE

Download Ideal Coordinates CCD File 
F [auth A], I [auth B], L [auth C](2~{S})-2-(3-azanylpropyl)-5-[2,5-bis(fluoranyl)phenyl]-~{N}-methoxy-~{N}-methyl-2-phenyl-1,3,4-thiadiazole-3-carboxamide
C20 H22 F2 N4 O2 S
LLXISKGBWFTGEI-FQEVSTJZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], H [auth B], K [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GCE BindingDB:  6HKY IC50: min: 6, max: 18 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.183 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.811α = 90
b = 95.811β = 90
c = 125.953γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Database references