4BXN

Eg5(WT) complex


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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 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 ...

    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".


    Organizational Affiliation

    The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BS, Scotland, U.K. s.talapatra@ed.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KINESIN-LIKE PROTEIN KIF11A, B368Homo 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
GTEx:  ENSG00000138160 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52732
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6LX
Query on 6LX

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
S [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CD
Query on CD

Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
D [auth A],
E [auth A],
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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
FA [auth B],
IA [auth B],
JA [auth B],
M [auth A],
O [auth A],
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 81.426α = 90
b = 81.426β = 90
c = 115.202γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
CCP4phasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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