NP-MRD: Showing NP-Card for (2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile (NP0219049)

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Record Information

Version

2.0

Created at

2022-09-05 19:55:12 UTC

Updated at

2022-09-05 19:55:12 UTC

NP-MRD ID

NP0219049

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile

Description

Osmaronin belongs to the class of organic compounds known as fatty acyl glycosides of mono- and disaccharides. Fatty acyl glycosides of mono- and disaccharides are compounds composed of a mono- or disaccharide moiety linked to one hydroxyl group of a fatty alcohol or of a phosphorylated alcohol (phosphoprenols), a hydroxy fatty acid or to one carboxyl group of a fatty acid (ester linkage) or to an amino alcohol. (2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile is found in Exochorda giraldii, Hordeum vulgare and Oemleria cerasiformis. (2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile was first documented in 2014 (PMID: 24952469). Based on a literature review very few articles have been published on Osmaronin (PMID: 27337134).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309052221552D          

 18 18  0  0  1  0            999 V2000
    0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  3  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
  8 17  1  0  0  0  0
 17 18  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0219049

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)=C\C#N

> <INCHI_IDENTIFIER>
InChI=1S/C11H17NO6/c1-6(2-3-12)5-17-11-10(16)9(15)8(14)7(4-13)18-11/h2,7-11,13-16H,4-5H2,1H3/b6-2-/t7-,8-,9+,10-,11-/m1/s1

> <INCHI_KEY>
DAVUWBZDLSJMFA-GMLQCYRESA-N

> <FORMULA>
C11H17NO6

> <MOLECULAR_WEIGHT>
259.258

> <EXACT_MASS>
259.105587271

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
25.227365639471905

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2Z)-3-methyl-4-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile

> <JCHEM_LOGP>
-1.6640477099999995

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.200070226410379

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.210510432071423

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810835523174575

> <JCHEM_POLAR_SURFACE_AREA>
123.17000000000002

> <JCHEM_REFRACTIVITY>
60.414199999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2Z)-3-methyl-4-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -4.001   5.390   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    2    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   17                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    8   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₇NO₆

Average Mass

259.2580 Da

Monoisotopic Mass

259.10559 Da

IUPAC Name

(2Z)-3-methyl-4-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile

Traditional Name

(2Z)-3-methyl-4-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile

CAS Registry Number

Not Available

SMILES

C\C(CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)=C\C#N

InChI Identifier

InChI=1S/C11H17NO6/c1-6(2-3-12)5-17-11-10(16)9(15)8(14)7(4-13)18-11/h2,7-11,13-16H,4-5H2,1H3/b6-2-/t7-,8-,9+,10-,11-/m1/s1

InChI Key

DAVUWBZDLSJMFA-GMLQCYRESA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Exochorda giraldii	LOTUS Database	35616633
Hordeum vulgare	LOTUS Database	35616633
Oemleria cerasiformis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty acyl glycosides of mono- and disaccharides. Fatty acyl glycosides of mono- and disaccharides are compounds composed of a mono- or disaccharide moiety linked to one hydroxyl group of a fatty alcohol or of a phosphorylated alcohol (phosphoprenols), a hydroxy fatty acid or to one carboxyl group of a fatty acid (ester linkage) or to an amino alcohol.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acyl glycosides

Direct Parent

Fatty acyl glycosides of mono- and disaccharides

Alternative Parents

Substituents

Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Monosaccharide
Oxane
Secondary alcohol
Acetal
Carbonitrile
Nitrile
Oxacycle
Organoheterocyclic compound
Polyol
Alcohol
Hydrocarbon derivative
Cyanide
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Organopnictogen compound
Primary alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.7	ChemAxon
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	123.17 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	60.41 m³·mol⁻¹	ChemAxon
Polarizability	25.23 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00057121

Chemspider ID

9207768

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11032594

PDB ID

Not Available

ChEBI ID

173851

Good Scents ID

Not Available

References

General References

Knoch E, Motawie MS, Olsen CE, Moller BL, Lyngkjaer MF: Biosynthesis of the leucine derived alpha-, beta- and gamma-hydroxynitrile glucosides in barley (Hordeum vulgare L.). Plant J. 2016 Oct;88(2):247-256. doi: 10.1111/tpj.13247. Epub 2016 Aug 31. [PubMed:27337134 ]
Guan B, Li T, Xu XK, Zhang XF, Wei PL, Peng CC, Fu JJ, Zeng Q, Cheng XR, Zhang SD, Yan SK, Jin HZ, Zhang WD: gamma-Hydroxynitrile glucosides from the seeds of Prinsepia utilis. Phytochemistry. 2014 Sep;105:135-40. doi: 10.1016/j.phytochem.2014.05.018. Epub 2014 Jun 18. [PubMed:24952469 ]
LOTUS database [Link]

Showing NP-Card for (2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile (NP0219049)

MOL for NP0219049 ((2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile)

3D MOL for NP0219049 ((2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile)

3D SDF for NP0219049 ((2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile)

3D-SDF for NP0219049 ((2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile)

PDB for NP0219049 ((2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile)

3D PDB for NP0219049 ((2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile)

SMILES for NP0219049 ((2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile)

INCHI for NP0219049 ((2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile)

Structure for NP0219049 ((2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile)

3D Structure for NP0219049 ((2z)-3-methyl-4-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}but-2-enenitrile)