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Showing NP-Card for Arabinonic acid (NP0044973)

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Record Information
Version2.0
Created at2022-03-10 18:52:04 UTC
Updated at2022-03-10 22:18:21 UTC
NP-MRD IDNP0044973
Secondary Accession NumbersNone
Natural Product Identification
Common NameArabinonic acid
DescriptionArabinonic acid or arabinic acid, belongs to the class of organic compounds known as sugar acids and derivatives. Arabinonic acid is an organic compound with molecular formula of C5H10O6. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group. Arabinonic acid is an acidic monosaccharide containing arabinose unit and which is obtained from gum arabic, in which it is present as salts. Arabinonic acid is one several acids that are known in cannabis plants (PMID: 6991645 ).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0044973 (Arabinonic acid)


  Mrv1652305052017402D          

 11 10  0  0  0  0            999 V2000
   -3.4819    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1964   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4819    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7674   -0.2008    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7674   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0530    0.2116    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0530    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3385   -0.2008    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3385   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6240    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0903   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  8  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  8  9  1  6  0  0  0
  6  7  1  6  0  0  0
  4  5  1  6  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
Download

3D MOL for NP0044973 (Arabinonic acid)

     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
    3.3497   -1.0914   -0.0840 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6168   -0.1020   -0.2939 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0693    1.1555    0.0458 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2761   -0.2512   -0.8981 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9941   -1.5885   -1.1719 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2712    0.3040    0.1094 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3704   -0.4481    1.2770 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1040    0.1746   -0.5175 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3642   -1.1572   -0.8369 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1601    0.5823    0.5087 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0112   -0.2493    1.5940 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4977    1.8010    0.5899 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2564    0.3475   -1.8198 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9940   -2.1111   -0.3473 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5049    1.3770    0.2644 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3212    0.1968    2.0347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1833    0.7922   -1.4080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6012   -1.2311   -1.7804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0726    1.6628    0.7502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1600    0.4372    0.0308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8653   -0.6008    1.9528 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0
 10  8  1  0
  8  9  1  0
  8  6  1  0
  6  7  1  0
  6  4  1  0
  4  5  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
 11 21  1  0
 10 19  1  0
 10 20  1  0
  8 17  1  6
  9 18  1  0
  6 15  1  1
  7 16  1  0
  4 13  1  6
  5 14  1  0
  3 12  1  0
M  END
Download

3D SDF for NP0044973 (Arabinonic acid)


  Mrv1652305052017402D          

 11 10  0  0  0  0            999 V2000
   -3.4819    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1964   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4819    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7674   -0.2008    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7674   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0530    0.2116    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0530    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3385   -0.2008    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3385   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6240    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0903   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  8  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  8  9  1  6  0  0  0
  6  7  1  6  0  0  0
  4  5  1  6  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0044973

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4-/m0/s1

> <INCHI_KEY>
QXKAIJAYHKCRRA-NUNKFHFFSA-N

> <FORMULA>
C5H10O6

> <MOLECULAR_WEIGHT>
166.1293

> <EXACT_MASS>
166.047738052

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.260703661659544

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S)-2,3,4,5-tetrahydroxypentanoic acid

> <ALOGPS_LOGP>
-2.48

> <JCHEM_LOGP>
-2.7794093686666668

> <ALOGPS_LOGS>
0.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.768659694136133

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.393139811550542

> <JCHEM_PKA_STRONGEST_BASIC>
-2.974562302797298

> <JCHEM_POLAR_SURFACE_AREA>
118.22000000000001

> <JCHEM_REFRACTIVITY>
32.3085

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.58e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-xylonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0044973 (Arabinonic acid)

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PDB for NP0044973 (Arabinonic acid)
HEADER    PROTEIN                                 05-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-MAY-20         0                                  
HETATM    1  C   UNK     0      -6.500   0.395   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -7.833  -0.375   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -6.500   1.935   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -5.166  -0.375   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -5.166  -1.915   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -3.832   0.395   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.832   1.935   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.499  -0.375   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.499  -1.915   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.165   0.395   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.169  -0.375   0.000  0.00  0.00           O+0
CONECT    1    4    3    2                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    6    5                                                  
CONECT    5    4                                                            
CONECT    6    4    8    7                                                  
CONECT    7    6                                                            
CONECT    8    6   10    9                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0044973 (Arabinonic acid)
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SMILES for NP0044973 (Arabinonic acid)
OC[C@H](O)[C@@H](O)[C@H](O)C(O)=O
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INCHI for NP0044973 (Arabinonic acid)
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4-/m0/s1
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View in JSmol
Synonyms
ValueSource
L-XylonateChEBI
L-Xylonic acidKegg
​L-xylonateGenerator
2,3,4,5-Tetrahydroxypentanoic acidHMDB
XylonateHMDB
Xylonic acidHMDB
D-Xylonic acidMeSH
Chemical FormulaC5H10O6
Average Mass166.1293 Da
Monoisotopic Mass166.04774 Da
IUPAC Name(2S,3R,4S)-2,3,4,5-tetrahydroxypentanoic acid
Traditional NameL-xylonic acid
CAS Registry Number4172-44-5
SMILES
OC[C@H](O)[C@@H](O)[C@H](O)C(O)=O
InChI Identifier
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4-/m0/s1
InChI KeyQXKAIJAYHKCRRA-NUNKFHFFSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Cannabis sativaNULL
      Not Available
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentSugar acids and derivatives  
Alternative Parents
Substituents
  • Pentose monosaccharide
    • 

  • Beta-hydroxy acid
    • 

  • Sugar acid
    • 

  • Short-chain hydroxy acid
    • 

  • Alpha-hydroxy acid
    • 

  • Fatty acid
    • 

  • Hydroxy acid
    • 

  • Monosaccharide
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Polyol
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.5ALOGPS
logP-2.8ChemAxon
logS0.19ALOGPS
pKa (Strongest Acidic)3.39ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area118.22 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.31 m³·mol⁻¹ChemAxon
Polarizability14.26 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0060256  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC05411  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkXylonic acid  
METLIN IDNot Available
PubChem Compound6971043  
PDB IDNot Available
ChEBI ID48092  
Good Scents IDNot Available
References
General References