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Showing metabocard for alpha-L-arabinofuranose (HMDB0304537)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 10:32:55 UTC
Update Date2021-09-24 10:32:56 UTC
HMDB IDHMDB0304537
Secondary Accession NumbersNone
Metabolite Identification
Common Namealpha-L-arabinofuranose
DescriptionAlpha-l-arabinose is a member of the class of compounds known as pentoses. Pentoses are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Alpha-l-arabinose is very soluble (in water) and a very weakly acidic compound (based on its pKa). Alpha-l-arabinose can be found in a number of food items such as cloudberry, amaranth, red beetroot, and white mustard, which makes alpha-l-arabinose a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304537 (alpha-L-arabinofuranose)


  Mrv0541 02231216432D          

 10 10  0  0  1  0            999 V2000
   -1.8897   -0.2077    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2766    0.3443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4920    0.0894    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1754    0.5743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8429    0.0894    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6275    0.3443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5879   -0.6952    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0729   -1.3627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2371   -0.6952    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7220   -1.3627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  6  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  1  0  0  0
M  END
Download

3D MOL for HMDB0304537 (alpha-L-arabinofuranose)

HMDB0304537
     RDKit          3D
alpha-L-arabinofuranose
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.5210   -1.5131    0.2653 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1146   -0.2870   -0.2659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8155    0.1791    0.3534 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4838    1.3785   -0.2134 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8493    1.4135   -0.4931 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4261    2.5388    0.0921 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4838    0.1301   -0.0836 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3712   -0.3494   -1.0347 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2833   -0.8040    0.0176 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4865   -1.7411    1.0187 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3621   -1.7513   -0.2162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9009    0.4812   -0.1046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9163   -0.3818   -1.3700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9003    0.3075    1.4441 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9764    1.5082   -1.6073 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7983    3.2979   -0.1259 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9826    0.1994    0.9192 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0253   -0.9781   -0.6373 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0859   -1.3277   -0.9438 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2459   -2.3006    0.7397 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  3  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  1
  5 15  1  6
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  6
 10 20  1  0
M  END
Download

3D SDF for HMDB0304537 (alpha-L-arabinofuranose)


  Mrv0541 02231216432D          

 10 10  0  0  1  0            999 V2000
   -1.8897   -0.2077    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2766    0.3443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4920    0.0894    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1754    0.5743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8429    0.0894    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6275    0.3443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5879   -0.6952    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0729   -1.3627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2371   -0.6952    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7220   -1.3627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  6  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0304537

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4+,5+/m0/s1

> <INCHI_KEY>
HMFHBZSHGGEWLO-QMKXCQHVSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
13.492672286939811

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5S)-5-(hydroxymethyl)oxolane-2,3,4-triol

> <ALOGPS_LOGP>
-2.65

> <JCHEM_LOGP>
-2.302204276

> <ALOGPS_LOGS>
0.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.899514700313038

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.30569577774193

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811390578102284

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
29.960899999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.07e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-L-arabinofuranose

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304537 (alpha-L-arabinofuranose)

HMDB0304537
     RDKit          3D
alpha-L-arabinofuranose
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.5210   -1.5131    0.2653 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1146   -0.2870   -0.2659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8155    0.1791    0.3534 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4838    1.3785   -0.2134 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8493    1.4135   -0.4931 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4261    2.5388    0.0921 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4838    0.1301   -0.0836 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3712   -0.3494   -1.0347 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2833   -0.8040    0.0176 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4865   -1.7411    1.0187 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3621   -1.7513   -0.2162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9009    0.4812   -0.1046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9163   -0.3818   -1.3700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9003    0.3075    1.4441 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9764    1.5082   -1.6073 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7983    3.2979   -0.1259 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9826    0.1994    0.9192 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0253   -0.9781   -0.6373 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0859   -1.3277   -0.9438 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2459   -2.3006    0.7397 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  3  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  1
  5 15  1  6
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  6
 10 20  1  0
M  END
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PDB for HMDB0304537 (alpha-L-arabinofuranose)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      -3.527  -0.388   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.383   0.643   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.918   0.167   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.327   1.072   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.573   0.167   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.038   0.643   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.097  -1.298   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.003  -2.544   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.443  -1.298   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.348  -2.544   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    3   10                                                  
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for HMDB0304537 (alpha-L-arabinofuranose)

COMPND    HMDB0304537
HETATM    1  O1  UNL     1      -2.521  -1.513   0.265  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.115  -0.287  -0.266  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.816   0.179   0.353  1.00  0.00           C  
HETATM    4  O2  UNL     1      -0.484   1.378  -0.213  1.00  0.00           O  
HETATM    5  C3  UNL     1       0.849   1.413  -0.493  1.00  0.00           C  
HETATM    6  O3  UNL     1       1.426   2.539   0.092  1.00  0.00           O  
HETATM    7  C4  UNL     1       1.484   0.130  -0.084  1.00  0.00           C  
HETATM    8  O4  UNL     1       2.371  -0.349  -1.035  1.00  0.00           O  
HETATM    9  C5  UNL     1       0.283  -0.804   0.018  1.00  0.00           C  
HETATM   10  O5  UNL     1       0.486  -1.741   1.019  1.00  0.00           O  
HETATM   11  H1  UNL     1      -3.362  -1.751  -0.216  1.00  0.00           H  
HETATM   12  H2  UNL     1      -2.901   0.481  -0.105  1.00  0.00           H  
HETATM   13  H3  UNL     1      -1.916  -0.382  -1.370  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.900   0.307   1.444  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.976   1.508  -1.607  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.798   3.298  -0.126  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.983   0.199   0.919  1.00  0.00           H  
HETATM   18  H8  UNL     1       3.025  -0.978  -0.637  1.00  0.00           H  
HETATM   19  H9  UNL     1       0.086  -1.328  -0.944  1.00  0.00           H  
HETATM   20  H10 UNL     1       1.246  -2.301   0.740  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3   12   13
CONECT    3    4    9   14
CONECT    4    5
CONECT    5    6    7   15
CONECT    6   16
CONECT    7    8    9   17
CONECT    8   18
CONECT    9   10   19
CONECT   10   20
END
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SMILES for HMDB0304537 (alpha-L-arabinofuranose)

OC[C@@H]1O[C@@H](O)[C@H](O)[C@H]1O
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INCHI for HMDB0304537 (alpha-L-arabinofuranose)

InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4+,5+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
WURCS=2.0/1,1,0/[a211h-1a_1-4]/1/ChEBI
a-L-ArabinoseGenerator
Α-L-arabinoseGenerator
alpha-L-ArabinoseChEBI
Chemical FormulaC5H10O5
Average Molecular Weight150.1299
Monoisotopic Molecular Weight150.05282343
IUPAC Name(2R,3R,4R,5S)-5-(hydroxymethyl)oxolane-2,3,4-triol
Traditional Nameα-L-arabinofuranose
CAS Registry NumberNot Available
SMILES
OC[C@@H]1O[C@@H](O)[C@H](O)[C@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4+,5+/m0/s1
InChI KeyHMFHBZSHGGEWLO-QMKXCQHVSA-N
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
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-2.6ALOGPS
logP-2.3ChemAxon
logS0.85ALOGPS
pKa (Strongest Acidic)11.31ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.96 m³·mol⁻¹ChemAxon
Polarizability13.49 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+134.29332859911
AllCCS[M+H-H2O]+129.8132859911
AllCCS[M+Na]+139.67932859911
AllCCS[M+NH4]+138.47332859911
AllCCS[M-H]-124.84532859911
AllCCS[M+Na-2H]-126.51232859911
AllCCS[M+HCOO]-128.39632859911
DeepCCS[M+H]+134.01230932474
DeepCCS[M-H]-131.69330932474
DeepCCS[M-2H]-166.06130932474
DeepCCS[M+Na]+140.29930932474

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - alpha-L-arabinofuranose GC-MS (Non-derivatized) - 70eV, Positivesplash10-05cu-9300000000-e24e80da64b2475ddfd82017-08-28Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-L-arabinofuranose 10V, Positive-QTOFsplash10-0ue9-2900000000-6c1199d377747f0e5b492017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-L-arabinofuranose 20V, Positive-QTOFsplash10-0f89-2900000000-8a9f89ac0a25c323249e2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-L-arabinofuranose 40V, Positive-QTOFsplash10-052p-9100000000-eaebbbf2fa629ce041602017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-L-arabinofuranose 10V, Negative-QTOFsplash10-0002-1900000000-6c48df798a58fc7029d92017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-L-arabinofuranose 20V, Negative-QTOFsplash10-001j-2900000000-816419eb5dad5bd998192017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-L-arabinofuranose 40V, Negative-QTOFsplash10-0006-9200000000-91d11d896b253dfd96932017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-L-arabinofuranose 10V, Positive-QTOFsplash10-0gc0-1900000000-346af5e1437ac746833b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-L-arabinofuranose 20V, Positive-QTOFsplash10-0nc4-9400000000-74fd6af917cb088bef2b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-L-arabinofuranose 40V, Positive-QTOFsplash10-0a4i-9000000000-55c82f4fa793a5fd288b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-L-arabinofuranose 10V, Negative-QTOFsplash10-0pc1-5900000000-6953077be254812d8b252021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-L-arabinofuranose 20V, Negative-QTOFsplash10-0a4i-9100000000-fcc3022a655e16f83b2c2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - alpha-L-arabinofuranose 40V, Negative-QTOFsplash10-0006-9000000000-750ecddfae4eefc719962021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB03142
Phenol Explorer Compound IDNot Available
FooDB IDFDB031274
KNApSAcK IDNot Available
Chemspider ID393416
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound445935
PDB IDNot Available
ChEBI ID28772
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available