6GF3

Tubulin-Jerantinine B acetate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


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Literature

Sustainable Syntheses of (-)-Jerantinines A & E and Structural Characterisation of the Jerantinine-Tubulin Complex at the Colchicine Binding Site.

Smedley, C.J.Stanley, P.A.Qazzaz, M.E.Prota, A.E.Olieric, N.Collins, H.Eastman, H.Barrow, A.S.Lim, K.H.Kam, T.S.Smith, B.J.Duivenvoorden, H.M.Parker, B.S.Bradshaw, T.D.Steinmetz, M.O.Moses, J.E.

(2018) Sci Rep 8: 10617-10617

  • DOI: https://doi.org/10.1038/s41598-018-28880-2
  • Primary Citation of Related Structures:  
    6GF3

  • PubMed Abstract: 

    The jerantinine family of Aspidosperma indole alkaloids from Tabernaemontana corymbosa are potent microtubule-targeting agents with broad spectrum anticancer activity. The natural supply of these precious metabolites has been significantly disrupted due to the inclusion of T. corymbosa on the endangered list of threatened species by the International Union for Conservation of Nature. This report describes the asymmetric syntheses of (-)-jerantinines A and E from sustainably sourced (-)-tabersonine, using a straight-forward and robust biomimetic approach. Biological investigations of synthetic (-)-jerantinine A, along with molecular modelling and X-ray crystallography studies of the tubulin-(-)-jerantinine B acetate complex, advocate an anticancer mode of action of the jerantinines operating via microtubule disruption resulting from binding at the colchicine site. This work lays the foundation for accessing useful quantities of enantiomerically pure jerantinine alkaloids for future development.


  • Organizational Affiliation

    La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain
A, C
451Bos taurusMutation(s): 0 
UniProt
Find proteins for P81947 (Bos taurus)
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81947
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-2B chain445Bos taurusMutation(s): 0 
UniProt
Find proteins for Q6B856 (Bos taurus)
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UniProt GroupQ6B856
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-2B chain445Bos taurusMutation(s): 0 
UniProt
Find proteins for Q6B856 (Bos taurus)
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UniProt GroupQ6B856
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Stathmin-4143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
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UniProt GroupP63043
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin tyrosine ligase384Gallus gallusMutation(s): 0 
Gene Names: TTL
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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G [auth A],
N [auth C]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP
Query on ACP

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U [auth F]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP
Query on GDP

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J [auth B],
R [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
EX5
Query on EX5

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L [auth B]Jerantinine B
C24 H28 N2 O6
ZWUDUCJVIQMXIN-YOQJOLSQSA-N
MES
Query on MES

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K [auth B],
T [auth D]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
EDO
Query on EDO

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Q [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

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I [auth A],
P [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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H [auth A],
M [auth B],
O [auth C],
S [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.72α = 90
b = 158.15β = 90
c = 180.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_166608

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description