NP-MRD: Showing NP-Card for Aldobiouronic acid D3 (NP0085001)

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Record Information

Version

2.0

Created at

2022-04-29 05:35:34 UTC

Updated at

2022-04-29 05:35:34 UTC

NP-MRD ID

NP0085001

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Aldobiouronic acid D3

Description

2-O-(Glucopyranosyluronic acid)xylose, also known as GA-2X, 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. Aldobiouronic acid D3 is found in Puya spp. Based on a literature review very few articles have been published on 2-O-(Glucopyranosyluronic acid)xylose.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 40  0  0  0  0  0  0  0  0999 V2000
    0.5925   -2.0883    2.7931 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3823   -1.3749    2.1766 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1757   -0.9649    0.7766 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0272   -1.4700    0.2843 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9174   -0.4365    0.0077 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2983   -0.5696   -1.3059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1723    0.3551   -1.7945 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5422    1.6605   -2.1486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3153    1.9023   -2.0134 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3111    2.7001   -2.6602 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3900    0.5363   -0.9333 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1783   -0.6141   -1.0895 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0441    0.6307    0.5351 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3947    1.8569    0.7183 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1439   -0.5300    0.8926 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8400   -1.7021    0.7329 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3089   -1.3016   -0.1519 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0578   -0.7367   -1.4291 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6558   -0.8571    0.2483 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1464   -1.2812    1.4485 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7563    0.6772    0.2591 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0938    1.0635    0.4183 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2532   -1.0575    2.7266 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0820    0.1389    0.7989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4336    0.5076    0.2501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5522   -0.0540   -2.7784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8067    3.2596   -1.9499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9808    1.3986   -1.2432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0461   -0.4831   -0.6620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9977    0.6288    1.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6551    2.2779    1.5533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8724   -0.3972    1.9689 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5529   -2.1301   -0.0919 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2990   -2.3977   -0.3140 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6144    0.1239   -1.2264 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4192   -1.1595   -0.5287 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5186   -0.5823    2.0212 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1038    1.1025    1.0488 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3738    1.0193   -0.7270 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6389    0.3485   -0.0218 H   0  0  0  0  0  0  0  0  0  0  0  0
 22 21  1  0
 21 19  1  0
 19 20  1  0
 19 17  1  0
 17 18  1  0
 17  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  7  8  1  0
  8 10  1  0
  8  9  2  0
  3  2  1  0
  2  1  2  0
 15  5  1  0
 22 40  1  0
 21 38  1  0
 21 39  1  0
 19 36  1  6
 20 37  1  0
 17 34  1  6
 18 35  1  0
  3 24  1  1
  5 25  1  6
  7 26  1  6
 11 28  1  6
 12 29  1  0
 13 30  1  1
 14 31  1  0
 15 32  1  1
 16 33  1  0
 10 27  1  0
  2 23  1  0
M  END


  Mrv1652304292207352D          

 22 22  0  0  1  0            999 V2000
    1.7309   -4.4270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3809   -4.4270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809   -2.9980    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9684   -2.2836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2059   -2.9980    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184   -2.2836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4434   -2.2836    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8559   -1.5691    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4434   -0.8546    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6809   -1.5691    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.0934   -0.8546    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0934   -2.2836    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.9184   -2.2836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6809   -2.9980    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8559   -2.9980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0934   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6809   -4.4270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9184   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2059   -4.4270    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  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  9  8  1  6  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  6  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
  9 17  1  0  0  0  0
 16 18  1  1  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
  7 21  1  0  0  0  0
 21 22  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0085001

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H](O)[C@H](O)[C@@H](O[C@H]1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O)C(O)=O)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H18O11/c12-1-3(14)5(15)4(2-13)21-11-8(18)6(16)7(17)9(22-11)10(19)20/h2-9,11-12,14-18H,1H2,(H,19,20)/t3-,4+,5+,6+,7+,8-,9+,11+/m1/s1

> <INCHI_KEY>
CXXAVRBGWUSLRR-MHNDCQGXSA-N

> <FORMULA>
C11H18O11

> <MOLECULAR_WEIGHT>
326.254

> <EXACT_MASS>
326.0849114

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
28.64040971067103

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[(2R,3S,4R)-3,4,5-trihydroxy-1-oxopentan-2-yl]oxy}oxane-2-carboxylic acid

> <ALOGPS_LOGP>
-2.48

> <JCHEM_LOGP>
-4.388586728666667

> <ALOGPS_LOGS>
-0.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.126732021855

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.210020984287819

> <JCHEM_PKA_STRONGEST_BASIC>
-3.523102215289911

> <JCHEM_POLAR_SURFACE_AREA>
194.20999999999998

> <JCHEM_REFRACTIVITY>
63.6638

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.49e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[(2R,3S,4R)-3,4,5-trihydroxy-1-oxopentan-2-yl]oxy}oxane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  O   UNK     0       3.231  -8.264   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.541  -6.930   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       6.311  -8.264   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       6.311  -5.596   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       5.541  -4.263   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       7.851  -5.596   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.621  -4.263   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      10.161  -4.263   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.931  -2.929   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      10.161  -1.595   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      12.471  -2.929   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      13.241  -1.595   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      13.241  -4.263   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      14.781  -4.263   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      12.471  -5.596   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      10.931  -5.596   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      13.241  -6.930   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      12.471  -8.264   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      14.781  -6.930   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       8.621  -6.930   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       7.851  -8.264   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   21                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   17                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16    9                                                       
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21    7   22                                                       
CONECT   22   21                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

View in JSmol

Synonyms

Value	Source
2-O-(Glucopyranosyluronate)xylose	Generator
2-O-(alpha-D-Glucopyranosyluronic acid)-D-xylose	MeSH
GA-2X	MeSH

Chemical Formula

C₁₁H₁₈O₁₁

Average Mass

326.2540 Da

Monoisotopic Mass

326.08491 Da

IUPAC Name

(2S,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[(2R,3S,4R)-3,4,5-trihydroxy-1-oxopentan-2-yl]oxy}oxane-2-carboxylic acid

Traditional Name

(2S,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[(2R,3S,4R)-3,4,5-trihydroxy-1-oxopentan-2-yl]oxy}oxane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

OC[C@@H](O)[C@H](O)[C@@H](O[C@H]1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O)C(O)=O)C=O

InChI Identifier

InChI=1S/C11H18O11/c12-1-3(14)5(15)4(2-13)21-11-8(18)6(16)7(17)9(22-11)10(19)20/h2-9,11-12,14-18H,1H2,(H,19,20)/t3-,4+,5+,6+,7+,8-,9+,11+/m1/s1

InChI Key

CXXAVRBGWUSLRR-MHNDCQGXSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Puya spp.	Plant	KNApSAcK

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
O-glucuronide
1-o-glucuronide
Glucuronic acid or derivatives
Alkyl glycoside
Glycosyl compound
O-glycosyl compound
Beta-hydroxy acid
Pyran
Beta-hydroxy aldehyde
Hydroxy acid
Oxane
Monosaccharide
Secondary alcohol
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Polyol
Organoheterocyclic compound
Oxacycle
Acetal
Carboxylic acid
Organic oxygen compound
Organooxygen compound
Carbonyl group
Primary alcohol
Hydrocarbon derivative
Organic oxide
Aldehyde
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	-2.5	ALOGPS
logP	-4.4	ChemAxon
logS	-0.34	ALOGPS
pKa (Strongest Acidic)	3.21	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	194.21 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	63.66 m³·mol⁻¹	ChemAxon
Polarizability	28.64 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	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

C00054671

Chemspider ID

4590914

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5492235

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Aldobiouronic acid D3 (NP0085001)

MOL for NP0085001 (Aldobiouronic acid D3)

3D MOL for NP0085001 (Aldobiouronic acid D3)

3D SDF for NP0085001 (Aldobiouronic acid D3)

3D-SDF for NP0085001 (Aldobiouronic acid D3)

PDB for NP0085001 (Aldobiouronic acid D3)

3D PDB for NP0085001 (Aldobiouronic acid D3)

SMILES for NP0085001 (Aldobiouronic acid D3)

INCHI for NP0085001 (Aldobiouronic acid D3)

Structure for NP0085001 (Aldobiouronic acid D3)

3D Structure for NP0085001 (Aldobiouronic acid D3)