8CI0

Maize Transketolase in complex with TPP and hydrolyzed (+)-Cornexistin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.153 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Investigations into Simplified Analogues of the Herbicidal Natural Product (+)-Cornexistin.

Steinborn, C.Tancredi, A.Habiger, C.Diederich, C.Kramer, J.Reingruber, A.M.Laber, B.Freigang, J.Lange, G.Schmutzler, D.Machettira, A.Besong, G.Magauer, T.Barber, D.M.

(2023) Chemistry 29: e202300199-e202300199

  • DOI: https://doi.org/10.1002/chem.202300199
  • Primary Citation of Related Structures:  
    8CI0

  • PubMed Abstract: 

    We report the design, synthesis and biological evaluation of simplified analogues of the herbicidal natural product (+)-cornexistin. Guided by an X-Ray co-crystal structure of cornexistin bound to transketolase from Zea mays, we attempted to identify the key interactions that are necessary for cornexistin to maintain its herbicidal profile. This resulted in the preparation of three novel analogues investigating the importance of substituents that are located on the nine-membered ring of cornexistin. One analogue maintained a good level of biological activity and could provide researchers insights in how to further optimize the structure of cornexistin for commercialization in the future.


  • Organizational Affiliation

    Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transketolase, chloroplasticA [auth AAA],
B [auth BBB],
C [auth CCC]
688Zea maysMutation(s): 0 
EC: 2.2.1.1
UniProt
Find proteins for Q7SIC9 (Zea mays)
Explore Q7SIC9 
Go to UniProtKB:  Q7SIC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIC9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8EL
Query on 8EL

Download Ideal Coordinates CCD File 
J [auth CCC]2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate
C12 H20 N4 O7 P2 S
FCUXBJDJFWOWMD-UHFFFAOYSA-N
TPP (Subject of Investigation/LOI)
Query on TPP

Download Ideal Coordinates CCD File 
E [auth AAA],
G [auth BBB]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
UP0 (Subject of Investigation/LOI)
Query on UP0

Download Ideal Coordinates CCD File 
H [auth CCC](1~{Z},3~{R},4~{S},7~{S},8~{Z})-8-ethylidene-4,7-bis(oxidanyl)-5-oxidanylidene-3-propyl-cyclononene-1,2-dicarboxylic acid
C16 H22 O7
YFQGJJCDYCWLSI-KRKAZGBPSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth AAA],
F [auth BBB],
I [auth CCC]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.153 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.309α = 90
b = 135.309β = 90
c = 201.439γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-03-22 
  • Deposition Author(s): Freigang, J.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references, Refinement description
  • Version 1.2: 2024-06-19
    Changes: Data collection