2WXD

A MICROMOLAR O-SULFATED THIOHYDROXIMATE INHIBITOR BOUND TO PLANT MYROSINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 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 Struct Biol Cryst Commun 66: 152

  • DOI: https://doi.org/10.1107/S1744309109052865
  • Primary Citation of Related Structures:  
    2WXD

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MYROSINASEA [auth M]501Sinapis albaMutation(s): 0 
EC: 3.2.3.1 (PDB Primary Data), 3.2.1.147 (UniProt)
UniProt
Find proteins for P29736 (Sinapis alba)
Explore P29736 
Go to UniProtKB:  P29736
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29736
Glycosylation
Glycosylation Sites: 10
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth A],
C [auth B],
F [auth E],
G [auth F]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G06206UV
GlyCosmos:  G06206UV
GlyGen:  G06206UV
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth D]7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G26295XE
GlyCosmos:  G26295XE
GlyGen:  G26295XE
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E18
Query on E18

Download Ideal Coordinates CCD File 
L [auth M]2-(DIMETHYLAMINO)ETHYL (1Z)-2-PHENYL-N-(SULFOOXY)ETHANIMIDOTHIOATE
C12 H18 N2 O4 S2
AJWBDCAFLSUABV-SEYXRHQNSA-N
NAG
Query on NAG

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H [auth M],
I [auth M],
J [auth M],
K [auth M]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
N [auth M]
O [auth M]
P [auth M]
Q [auth M]
R [auth M]
N [auth M],
O [auth M],
P [auth M],
Q [auth M],
R [auth M],
S [auth M],
T [auth M]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
U [auth M],
V [auth M],
W [auth M],
X [auth M]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
E18 PDBBind:  2WXD IC50: 3300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.245α = 90
b = 137.567β = 90
c = 80.723γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2012-04-04
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-09
    Changes: Structure summary