2WXD

A MICROMOLAR O-SULFATED THIOHYDROXIMATE INHIBITOR BOUND TO PLANT MYROSINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Micromolar O-Sulfated Thiohydroximate Inhibitor Bound to Plant Myrosinase

Besle, A.Brazzolotto, X.Tatibouet, A.Cerniauskaite, D.Gallienne, E.Rollin, P.Burmeister, W.P.

(2010) Acta Crystallogr.,Sect.F 66: 152

  • DOI: 10.1107/S1744309109052865

  • PubMed Abstract: 
  • The 1.6 A resolution structure of the micromolar competitive inhibitor S-(N,N-dimethylaminoethyl) phenylacetothiohydroximate-O-sulfate bound to Sinapis alba myrosinase, a plant thioglucosidase, is reported. Myrosinase and its substrates, the glucosin ...

    The 1.6 A resolution structure of the micromolar competitive inhibitor S-(N,N-dimethylaminoethyl) phenylacetothiohydroximate-O-sulfate bound to Sinapis alba myrosinase, a plant thioglucosidase, is reported. Myrosinase and its substrates, the glucosinolates, are part of the plant's defence system. The sulfate group and the phenyl group of the inhibitor bind to the aglycon-binding site of the enzyme, whereas the N,N-dimethyl group binds to the glucose-binding site and explains the large improvement in binding affinity compared with previous compounds. The structure suggests ways to increase the potency and specificity of the compound by improving the interactions with the hydrophobic pocket of the aglycon-binding site.


    Related Citations: 
    • A Simple O-Sulfated Thiohydroximate Molecule to be the First Micromolar Range Myrosinase Inhibitor
      Cerniauskaite, D.,Gallienne, E.,Karciauskaite, H.,Farinha, A.S.F.,Rousseau, J.,Armand, S.,Tatibouet, A.,Sackus, A.,Rollin, P.
      (2009) Tetrahedron Letters 50: 3302


    Organizational Affiliation

    UJF-EMBL-CNRS UMI 3265, Unit of Virus Host Cell Interactions, BP 181, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYROSINASE
M
501Sinapis albaMutation(s): 0 
EC: 3.2.1.147
Find proteins for P29736 (Sinapis alba)
Go to UniProtKB:  P29736
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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M
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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M
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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M
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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M
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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M
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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M
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
XYP
Query on XYP

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M
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
E18
Query on E18

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M
2-(DIMETHYLAMINO)ETHYL (1Z)-2-PHENYL-N-(SULFOOXY)ETHANIMIDOTHIOATE
C12 H18 N2 O4 S2
AJWBDCAFLSUABV-SEYXRHQNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
E18IC50: 3300 nM BINDINGMOAD
E18IC50: 3300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.143 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 136.245α = 90.00
b = 137.567β = 90.00
c = 80.723γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2012-04-04
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance