Np mrd loader

Showing NP-Card for D-Apiose (NP0045490)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2022-03-17 19:20:51 UTC
Updated at2022-03-17 19:20:52 UTC
NP-MRD IDNP0045490
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Apiose
DescriptionD-Apiose, also known as apiose or (R)-form, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Apiose is a branched-chain sugar found as residues in galacturonans-type pectins; that occurs in parsley and many other plants. D-Apiose is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, D-Apiose has been detected, but not quantified in, parsley. This could make D-apiose a potential biomarker for the consumption of these foods. Apiose is a component of cell wall polysaccharides. Apiose 1-reductase uses D-apiitol and NAD+ to produce apiitol-apiose, NADH, and H+. D-Apiose is found in Lemna minor, Posidonia australis, Wolffia arrhiza and Zostera nana. Flavone apiosyltransferase uses UDP-apiose and 5,7,4'-trihydroxyflavone 7-O-β-D-glucoside to produce UDP, 5,7,4'-trihydroxyflavone (apigenin), and 7-O-β-D-apiosyl-(1->2)-β-apiitol-glucoside.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0045490 (D-Apiose)


  Mrv0541 02241211412D          

 10 10  0  0  0  0            999 V2000
    0.2034    1.5480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0411    0.7330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3663    0.0811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1812    0.1626    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8553    0.4886    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8553   -0.3256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0411   -0.5701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6108   -1.0590    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3663   -1.3850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1812   -1.5480    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
  2  5  1  0  0  0  0
  3  4  1  0  0  0  0
  3  7  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
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
Download

3D MOL for NP0045490 (D-Apiose)

Download
3D SDF for NP0045490 (D-Apiose)

  Mrv0541 02241211412D          

 10 10  0  0  0  0            999 V2000
    0.2034    1.5480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0411    0.7330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3663    0.0811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1812    0.1626    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8553    0.4886    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8553   -0.3256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0411   -0.5701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6108   -1.0590    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3663   -1.3850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1812   -1.5480    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
  2  5  1  0  0  0  0
  3  4  1  0  0  0  0
  3  7  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
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0045490

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1(O)COC(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-1-5(9)2-10-4(8)3(5)7/h3-4,6-9H,1-2H2

> <INCHI_KEY>
ASNHGEVAWNWCRQ-UHFFFAOYSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
13.47023338252624

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-(hydroxymethyl)oxolane-2,3,4-triol

> <ALOGPS_LOGP>
-2.20

> <JCHEM_LOGP>
-2.438202632333333

> <ALOGPS_LOGS>
0.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.313484061269477

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.235590710262377

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1423746812033153

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
30.1803

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.29e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-(hydroxymethyl)oxolane-2,3,4-triol

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0045490 (D-Apiose)
Download
PDB for NP0045490 (D-Apiose)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       0.380   2.890   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.077   1.368   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.684   0.151   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.205   0.304   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -1.597   0.912   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.597  -0.608   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.077  -1.064   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.140  -1.977   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.684  -2.585   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.205  -2.890   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    5                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7                                                       
CONECT    7    3    6    8    9                                             
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

Download
3D PDB for NP0045490 (D-Apiose)
Download
SMILES for NP0045490 (D-Apiose)
OCC1(O)COC(O)C1O
Download
INCHI for NP0045490 (D-Apiose)
InChI=1S/C5H10O5/c6-1-5(9)2-10-4(8)3(5)7/h3-4,6-9H,1-2H2
Download
View in JSmol
Synonyms
ValueSource
(R)-FormHMDB
3-C-HydroxymethyltetroseHMDB
ApioseHMDB
Apiose, 9ci, 8ciHMDB
b-D-ApiofuranoseGenerator
Β-D-apiofuranoseGenerator
Chemical FormulaC5H10O5
Average Mass150.1299 Da
Monoisotopic Mass150.05282 Da
IUPAC Name4-(hydroxymethyl)oxolane-2,3,4-triol
Traditional Name4-(hydroxymethyl)oxolane-2,3,4-triol
CAS Registry Number639-97-4
SMILES
OCC1(O)COC(O)C1O
InChI Identifier
InChI=1S/C5H10O5/c6-1-5(9)2-10-4(8)3(5)7/h3-4,6-9H,1-2H2
InChI KeyASNHGEVAWNWCRQ-UHFFFAOYSA-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
Lemna minorPlant
Petroselinum crispumFooDB
Posidonia australisPlant
Wolffia arrhizaPlant
Zostera nanaPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentPentoses  
Alternative Parents
Substituents
  • Pentose monosaccharide
    • 

  • Tetrahydrofuran
    • 

  • Tertiary alcohol
    • 

  • Secondary alcohol
    • 

  • Hemiacetal
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Polyol
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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-2.2ALOGPS
logP-2.4ChemAxon
logS0.94ALOGPS
pKa (Strongest Acidic)11.24ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity30.18 m³·mol⁻¹ChemAxon
Polarizability13.47 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0029941  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB001215  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC01488  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkApiose  
METLIN IDNot Available
PubChem Compound4479683  
PDB IDNot Available
ChEBI ID27672  
Good Scents IDNot Available
References
General ReferencesNot Available