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Showing metabocard for D-Arabinono-1,4-lactone (HMDB0302833)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 21:01:35 UTC
Update Date2021-09-23 21:01:35 UTC
HMDB IDHMDB0302833
Secondary Accession NumbersNone
Metabolite Identification
Common NameD-Arabinono-1,4-lactone
DescriptionD-arabinono-1,4-lactone, also known as D-arabinonic acid, gamma-lactone, is a member of the class of compounds known as pentoses. Pentoses are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-arabinono-1,4-lactone is soluble (in water) and a very weakly acidic compound (based on its pKa). D-arabinono-1,4-lactone can be found in rice, which makes D-arabinono-1,4-lactone a potential biomarker for the consumption of this food product. D-arabinono-1,4-lactone may be a unique S.cerevisiae (yeast) metabolite.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302833 (D-Arabinono-1,4-lactone)


  Mrv0541 02241212592D          

 10 10  0  0  1  0            999 V2000
   -1.1768    0.7682    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5638    1.3202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2209    1.0653    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8883    1.5502    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5557    1.0653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3404    1.3202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3008    0.2807    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7857   -0.3868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4758    0.2807    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0091   -0.3868    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  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  6  0  0  0
M  END
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3D MOL for HMDB0302833 (D-Arabinono-1,4-lactone)

HMDB0302833
     RDKit          3D
D-Arabinono-1,4-lactone
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.3799   -2.0466    0.7733 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4788   -1.1711    0.7395 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1381   -1.2898    1.0777 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6062   -0.1934    0.6282 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8015   -0.6991   -0.1294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6097    0.3184   -0.6201 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3174    0.6367   -0.2253 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1674    1.9957   -0.0348 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6800    0.2256    0.3120 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6820    0.3635   -0.6359 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9481    0.4017    1.4758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4024   -1.3099    0.5758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5271   -1.3598   -0.9716 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5621    0.2152   -0.3461 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2715    0.3805   -1.2997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0466    2.4907   -0.8851 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9178    0.8361    1.2126 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3774    0.2054   -1.5577 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  4  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  4 11  1  1
  5 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  6
  8 16  1  0
  9 17  1  1
 10 18  1  0
M  END
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3D SDF for HMDB0302833 (D-Arabinono-1,4-lactone)


  Mrv0541 02241212592D          

 10 10  0  0  1  0            999 V2000
   -1.1768    0.7682    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5638    1.3202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2209    1.0653    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8883    1.5502    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5557    1.0653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3404    1.3202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3008    0.2807    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7857   -0.3868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4758    0.2807    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0091   -0.3868    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  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0302833

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O5/c6-1-2-3(7)4(8)5(9)10-2/h2-4,6-8H,1H2/t2-,3-,4+/m1/s1

> <INCHI_KEY>
CUOKHACJLGPRHD-JJYYJPOSSA-N

> <FORMULA>
C5H8O5

> <MOLECULAR_WEIGHT>
148.114

> <EXACT_MASS>
148.037173366

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
12.808364958102313

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-one

> <ALOGPS_LOGP>
-1.98

> <JCHEM_LOGP>
-2.114938244

> <ALOGPS_LOGS>
0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.66228265576019

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.633837675631321

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9894265691123385

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
28.8163

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.47e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-arabinono-1,4-lactone

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0302833 (D-Arabinono-1,4-lactone)

HMDB0302833
     RDKit          3D
D-Arabinono-1,4-lactone
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.3799   -2.0466    0.7733 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4788   -1.1711    0.7395 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1381   -1.2898    1.0777 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6062   -0.1934    0.6282 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8015   -0.6991   -0.1294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6097    0.3184   -0.6201 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3174    0.6367   -0.2253 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1674    1.9957   -0.0348 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6800    0.2256    0.3120 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6820    0.3635   -0.6359 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9481    0.4017    1.4758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4024   -1.3099    0.5758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5271   -1.3598   -0.9716 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5621    0.2152   -0.3461 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2715    0.3805   -1.2997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0466    2.4907   -0.8851 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9178    0.8361    1.2126 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3774    0.2054   -1.5577 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  4  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  4 11  1  1
  5 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  6
  8 16  1  0
  9 17  1  1
 10 18  1  0
M  END
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PDB for HMDB0302833 (D-Arabinono-1,4-lactone)

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      -2.197   1.434   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.052   2.464   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.412   1.989   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.658   2.894   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.904   1.989   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.369   2.464   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.428   0.524   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.333  -0.722   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.888   0.524   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.017  -0.722   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 HMDB0302833 (D-Arabinono-1,4-lactone)

COMPND    HMDB0302833
HETATM    1  O1  UNL     1       2.380  -2.047   0.773  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.479  -1.171   0.740  1.00  0.00           C  
HETATM    3  O2  UNL     1       0.138  -1.290   1.078  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.606  -0.193   0.628  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.801  -0.699  -0.129  1.00  0.00           C  
HETATM    6  O3  UNL     1      -2.610   0.318  -0.620  1.00  0.00           O  
HETATM    7  C4  UNL     1       0.317   0.637  -0.225  1.00  0.00           C  
HETATM    8  O4  UNL     1       0.167   1.996  -0.035  1.00  0.00           O  
HETATM    9  C5  UNL     1       1.680   0.226   0.312  1.00  0.00           C  
HETATM   10  O5  UNL     1       2.682   0.364  -0.636  1.00  0.00           O  
HETATM   11  H1  UNL     1      -0.948   0.402   1.476  1.00  0.00           H  
HETATM   12  H2  UNL     1      -2.402  -1.310   0.576  1.00  0.00           H  
HETATM   13  H3  UNL     1      -1.527  -1.360  -0.972  1.00  0.00           H  
HETATM   14  H4  UNL     1      -3.562   0.215  -0.346  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.271   0.381  -1.300  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.047   2.491  -0.885  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.918   0.836   1.213  1.00  0.00           H  
HETATM   18  H8  UNL     1       2.377   0.205  -1.558  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    9
CONECT    3    4
CONECT    4    5    7   11
CONECT    5    6   12   13
CONECT    6   14
CONECT    7    8    9   15
CONECT    8   16
CONECT    9   10   17
CONECT   10   18
END
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SMILES for HMDB0302833 (D-Arabinono-1,4-lactone)

OC[C@H]1OC(=O)[C@@H](O)[C@@H]1O
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INCHI for HMDB0302833 (D-Arabinono-1,4-lactone)

InChI=1S/C5H8O5/c6-1-2-3(7)4(8)5(9)10-2/h2-4,6-8H,1H2/t2-,3-,4+/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,4-D-ArabinonolactoneChEBI
D-Arabinonic acid, gamma-lactoneChEBI
D-ArabonolactoneChEBI
D-Arabinonate, g-lactoneGenerator
D-Arabinonate, gamma-lactoneGenerator
D-Arabinonate, γ-lactoneGenerator
D-Arabinonic acid, g-lactoneGenerator
D-Arabinonic acid, γ-lactoneGenerator
Chemical FormulaC5H8O5
Average Molecular Weight148.114
Monoisotopic Molecular Weight148.037173366
IUPAC Name(3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-one
Traditional NameD-arabinono-1,4-lactone
CAS Registry NumberNot Available
SMILES
OC[C@H]1OC(=O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H8O5/c6-1-2-3(7)4(8)5(9)10-2/h2-4,6-8H,1H2/t2-,3-,4+/m1/s1
InChI KeyCUOKHACJLGPRHD-JJYYJPOSSA-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
  • Gamma butyrolactone
  • Tetrahydrofuran
  • Carboxylic acid ester
  • Lactone
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Oxacycle
  • Organoheterocyclic compound
  • Primary alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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-2ALOGPS
logP-2.1ChemAxon
logS0.76ALOGPS
pKa (Strongest Acidic)11.63ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.99 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity28.82 m³·mol⁻¹ChemAxon
Polarizability12.81 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]+133.28332859911
AllCCS[M+H-H2O]+128.77932859911
AllCCS[M+Na]+138.69632859911
AllCCS[M+NH4]+137.48432859911
AllCCS[M-H]-123.92532859911
AllCCS[M+Na-2H]-125.55632859911
AllCCS[M+HCOO]-127.432859911
DeepCCS[M+H]+131.76430932474
DeepCCS[M-H]-129.54930932474
DeepCCS[M-2H]-164.17930932474
DeepCCS[M+Na]+138.62230932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202210.1667 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.2 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid802.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid359.0 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid42.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid210.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid82.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid284.7 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid266.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)673.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid634.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid54.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid904.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid220.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid268.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate721.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA284.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water355.1 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra
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 IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB006401
KNApSAcK IDNot Available
Chemspider ID16751
KEGG Compound IDC00652
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound17723
PDB IDNot Available
ChEBI ID16292
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