NP-MRD: Showing NP-Card for threo-1-C-Syringylglycerol (NP0138546)

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Record Information

Version

1.0

Created at

2022-06-29 17:34:32 UTC

Updated at

2022-06-29 17:34:32 UTC

NP-MRD ID

NP0138546

Secondary Accession Numbers

None

Natural Product Identification

Common Name

threo-1-C-Syringylglycerol

Description

Threo-Syringoylglycerol, also known as threo-form, belongs to the class of organic compounds known as methoxyphenols. Methoxyphenols are compounds containing a methoxy group attached to the benzene ring of a phenol moiety. Threo-Syringoylglycerol is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, threo-Syringoylglycerol has been detected, but not quantified in, a few different foods, such as alcoholic beverages, coffee and coffee products, and tea. threo-1-C-Syringylglycerol is found in Magnolia grandiflora. This could make threo-syringoylglycerol a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 33  0  0  0  0  0  0  0  0999 V2000
   -1.7619    3.4631    0.5489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4912    2.2569    0.4450 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9042    1.0188    0.3366 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5363    0.8850    0.3232 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0890   -0.3458    0.2153 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5377   -0.5272    0.1974 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9120   -1.4326   -0.8192 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3183    0.7474    0.1118 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1472    1.4166   -1.0896 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7970    0.4112    0.2154 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2382   -0.3857   -0.8147 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7281   -1.4538    0.1200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1087   -1.3555    0.1303 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8878   -2.4887    0.0328 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2721   -3.7575   -0.0784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6940   -0.1073    0.2396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0964    0.0269    0.2532 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4141    4.3442    0.4550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9109    3.4815   -0.1700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3079    3.4785    1.5641 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0571    1.7805    0.4004 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8316   -1.0295    1.1486 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5286   -1.1830   -1.6931 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0645    1.3725    0.9648 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0050    1.7885   -1.4526 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0295   -0.0991    1.1752 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4224    1.3425    0.2126 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2517    0.0796   -1.6918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3069   -2.4664    0.0313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6151   -3.9211    0.8006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0782   -4.5022   -0.1364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6060   -3.7842   -0.9841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5099    0.9460    0.3336 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  2  0
 16 17  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 16  3  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  4 21  1  0
 12 29  1  0
 15 30  1  0
 15 31  1  0
 15 32  1  0
 17 33  1  0
  6 22  1  1
  7 23  1  0
  8 24  1  1
  9 25  1  0
 10 26  1  0
 10 27  1  0
 11 28  1  0
M  END


  Mrv0541 05061305492D          

 17 17  0  0  0  0            999 V2000
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    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    1.2375    0.0000 C   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
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 O   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
    1.4289    2.4750    0.0000 O   0  0  0  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
    2.1434   -0.4125    0.0000 O   0  0  0  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
  6  3  2  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  2  0  0  0  0
 10  6  1  0  0  0  0
 10  7  1  0  0  0  0
 11  8  2  0  0  0  0
 11  9  1  0  0  0  0
 12  5  1  0  0  0  0
 13  7  1  0  0  0  0
 14 10  1  0  0  0  0
 15 11  1  0  0  0  0
 16  1  1  0  0  0  0
 16  8  1  0  0  0  0
 17  2  1  0  0  0  0
 17  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0138546

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC(OC)=C1O)C(O)C(O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C11H16O6/c1-16-8-3-6(10(14)7(13)5-12)4-9(17-2)11(8)15/h3-4,7,10,12-15H,5H2,1-2H3

> <INCHI_KEY>
GIZSHQYTTBQKOQ-UHFFFAOYSA-N

> <FORMULA>
C11H16O6

> <MOLECULAR_WEIGHT>
244.2411

> <EXACT_MASS>
244.094688244

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
24.257727087579788

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-(4-hydroxy-3,5-dimethoxyphenyl)propane-1,2,3-triol

> <ALOGPS_LOGP>
-0.76

> <JCHEM_LOGP>
-0.6736816883333331

> <ALOGPS_LOGS>
-1.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.091049264840333

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.300919115423483

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9773032276802063

> <JCHEM_POLAR_SURFACE_AREA>
99.38000000000001

> <JCHEM_REFRACTIVITY>
59.70620000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.13e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-(4-hydroxy-3,5-dimethoxyphenyl)propane-1,2,3-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334   6.930   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
CONECT    1   16                                                            
CONECT    2   17                                                            
CONECT    3    6    8                                                       
CONECT    4    6    9                                                       
CONECT    5    7   12                                                       
CONECT    6    3    4   10                                                  
CONECT    7    5   10   13                                                  
CONECT    8    3   11   16                                                  
CONECT    9    4   11   17                                                  
CONECT   10    6    7   14                                                  
CONECT   11    8    9   15                                                  
CONECT   12    5                                                            
CONECT   13    7                                                            
CONECT   14   10                                                            
CONECT   15   11                                                            
CONECT   16    1    8                                                       
CONECT   17    2    9                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

View in JSmol

Synonyms

Value	Source
Syringoylglycerol	HMDB
Threo-form	HMDB

Chemical Formula

C₁₁H₁₆O₆

Average Mass

244.2411 Da

Monoisotopic Mass

244.09469 Da

IUPAC Name

1-(4-hydroxy-3,5-dimethoxyphenyl)propane-1,2,3-triol

Traditional Name

1-(4-hydroxy-3,5-dimethoxyphenyl)propane-1,2,3-triol

CAS Registry Number

121748-11-6

SMILES

COC1=CC(=CC(OC)=C1O)C(O)C(O)CO

InChI Identifier

InChI=1S/C11H16O6/c1-16-8-3-6(10(14)7(13)5-12)4-9(17-2)11(8)15/h3-4,7,10,12-15H,5H2,1-2H3

InChI Key

GIZSHQYTTBQKOQ-UHFFFAOYSA-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
Magnolia grandiflora	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as methoxyphenols. Methoxyphenols are compounds containing a methoxy group attached to the benzene ring of a phenol moiety.

Kingdom

Super Class

Class

Sub Class

Direct Parent

Alternative Parents

Substituents

M-dimethoxybenzene
Dimethoxybenzene
Methoxyphenol
Phenoxy compound
Anisole
Methoxybenzene
Phenol ether
Alkyl aryl ether
Monocyclic benzene moiety
Sugar alcohol
Secondary alcohol
Ether
Polyol
Primary alcohol
Alcohol
Aromatic alcohol
Hydrocarbon derivative
Organooxygen compound
Organic oxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

phenols (CHEBI:86807 )
methoxybenzene (CHEBI:86807 )

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	-0.76	ALOGPS
logP	-0.67	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	9.3	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	99.38 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	59.71 m³·mol⁻¹	ChemAxon
Polarizability	24.26 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

HMDB0031237

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB003263

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14237629

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for threo-1-C-Syringylglycerol (NP0138546)

MOL for NP0138546 (threo-1-C-Syringylglycerol)

3D MOL for NP0138546 (threo-1-C-Syringylglycerol)

3D SDF for NP0138546 (threo-1-C-Syringylglycerol)

3D-SDF for NP0138546 (threo-1-C-Syringylglycerol)

PDB for NP0138546 (threo-1-C-Syringylglycerol)

3D PDB for NP0138546 (threo-1-C-Syringylglycerol)

SMILES for NP0138546 (threo-1-C-Syringylglycerol)

INCHI for NP0138546 (threo-1-C-Syringylglycerol)

Structure for NP0138546 (threo-1-C-Syringylglycerol)

3D Structure for NP0138546 (threo-1-C-Syringylglycerol)