NP-MRD: Showing NP-Card for 2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid (NP0304441)

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Record Information

Version

2.0

Created at

2022-09-10 19:32:28 UTC

Updated at

2022-09-10 19:32:28 UTC

NP-MRD ID

NP0304441

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid

Description

2-{[3,4,5-Trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid 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. 2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid is found in Morchella deliciosa. 2-{[3,4,5-Trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 36  0  0  0  0  0  0  0  0999 V2000
    4.5496   -2.6658   -1.8655 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9067   -2.0326   -0.9763 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4911   -1.9386    0.2694 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5928   -1.4170   -1.2314 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2388   -0.4234   -0.1691 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0117    0.1670   -0.3272 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1414    0.0818    0.7295 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8078   -0.8867    0.2952 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7765   -0.2194   -0.4472 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5576   -1.1394   -1.3399 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2235   -2.1244   -0.6145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7155    0.3433    0.5997 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1168   -0.6946    1.4553 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9471    1.3972    1.3282 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4472    2.6361    0.8907 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4608    1.3148    1.2377 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0537    2.4707    0.5219 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2267    0.6892   -0.2924 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4674    0.5609   -0.2132 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8107    2.0205   -0.5164 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2778   -2.5026    1.0642 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6325   -0.9238   -2.2224 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8747   -2.2510   -1.3280 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4260   -0.9021    0.8075 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6616   -0.4718    1.5476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3671    0.6087   -1.0503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3440   -0.5186   -1.8506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9507   -1.6273   -2.1125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1305   -2.3207   -0.9677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6345    0.7465    0.1366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0983   -0.6893    1.5936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3025    1.3205    2.4026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6687    3.2130    1.6370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0720    1.5301    2.2821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7399    2.7590   -0.1048 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1051    2.2639   -1.1694 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  5 18  1  0
 18 20  1  0
 18 19  2  0
  7 16  1  0
 16 17  1  0
 16 14  1  0
 14 15  1  0
 14 12  1  0
 12 13  1  0
 12  9  1  0
 11 29  1  0
 10 27  1  0
 10 28  1  0
  9 26  1  6
  7 25  1  1
  5 24  1  1
  4 22  1  0
  4 23  1  0
  3 21  1  0
 20 36  1  0
 16 34  1  1
 17 35  1  0
 14 32  1  1
 15 33  1  0
 12 30  1  6
 13 31  1  0
M  END


  Mrv1533004201504312D          

 20 20  0  0  0  0            999 V2000
   -3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   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
   -0.7145   -0.4125    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
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    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
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  7 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
  5 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
  3 19  1  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0304441

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC(CC(O)=O)C(O)=O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C10H16O10/c11-2-4-6(14)7(15)8(16)10(20-4)19-3(9(17)18)1-5(12)13/h3-4,6-8,10-11,14-16H,1-2H2,(H,12,13)(H,17,18)

> <INCHI_KEY>
OCIAPZWBJQRATB-UHFFFAOYSA-N

> <FORMULA>
C10H16O10

> <MOLECULAR_WEIGHT>
296.228

> <EXACT_MASS>
296.074346715

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
25.89059885321672

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid

> <ALOGPS_LOGP>
-2.03

> <JCHEM_LOGP>
-2.884477073666667

> <ALOGPS_LOGS>
-0.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.101081270293712

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.272986259153279

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810837108995054

> <JCHEM_POLAR_SURFACE_AREA>
173.98

> <JCHEM_REFRACTIVITY>
57.2885

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.02e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-15         0                                  
HETATM    1  O   UNK     0      -6.668  -0.770   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.334  -0.770   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      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -6.668  -5.390   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   19                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   15                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    7   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    5   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17    3   20                                                  
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol

Synonyms

Value	Source
2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioate	Generator
(2S)-2-[(b-D-Glucopyranosyl)oxy]butanedioate	Generator
(2S)-2-[(b-D-Glucopyranosyl)oxy]butanedioic acid	Generator
(2S)-2-[(beta-D-Glucopyranosyl)oxy]butanedioate	Generator
(2S)-2-[(Β-D-glucopyranosyl)oxy]butanedioate	Generator
(2S)-2-[(Β-D-glucopyranosyl)oxy]butanedioic acid	Generator

Chemical Formula

C₁₀H₁₆O₁₀

Average Mass

296.2280 Da

Monoisotopic Mass

296.07435 Da

IUPAC Name

2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid

Traditional Name

2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid

CAS Registry Number

Not Available

SMILES

OCC1OC(OC(CC(O)=O)C(O)=O)C(O)C(O)C1O

InChI Identifier

InChI=1S/C10H16O10/c11-2-4-6(14)7(15)8(16)10(20-4)19-3(9(17)18)1-5(12)13/h3-4,6-8,10-11,14-16H,1-2H2,(H,12,13)(H,17,18)

InChI Key

OCIAPZWBJQRATB-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
Morchella deliciosa	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
Glycosyl compound
O-glycosyl compound
Heterocyclic fatty acid
Hydroxy fatty acid
Sugar acid
Fatty acid
Dicarboxylic acid or derivatives
Monosaccharide
Oxane
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Carboxylic acid
Acetal
Polyol
Organic oxygen compound
Primary alcohol
Organic oxide
Alcohol
Carbonyl group
Hydrocarbon derivative
Organooxygen compound
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	-2	ALOGPS
logP	-2.9	ChemAxon
logS	-0.46	ALOGPS
pKa (Strongest Acidic)	3.27	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	173.98 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	57.29 m³·mol⁻¹	ChemAxon
Polarizability	25.89 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

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

14484618

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid (NP0304441)

MOL for NP0304441 (2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid)

3D MOL for NP0304441 (2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid)

3D SDF for NP0304441 (2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid)

3D-SDF for NP0304441 (2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid)

PDB for NP0304441 (2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid)

3D PDB for NP0304441 (2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid)

SMILES for NP0304441 (2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid)

INCHI for NP0304441 (2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid)

Structure for NP0304441 (2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid)

3D Structure for NP0304441 (2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanedioic acid)