Showing metabocard for D-arabinono-1,4-lactone (MMDBc0054421)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 23:11:41 UTC
Update Date2022-08-12 20:09:00 UTC
Metabolite IDMMDBc0054421
Metabolite Identification
Common NameD-arabinono-1,4-lactone
DescriptionD-arabinono-1,4-lactone belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-arabinono-1,4-lactone is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on D-arabinono-1,4-lactone.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fece848d6e0>


  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 #<Metabolite:0x00007fece848d6e0>

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 #<Metabolite:0x00007fece848d6e0>


  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>
MMDBc0054421

> <DATABASE_NAME>
MIME

> <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

$$$$
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3D-SDF for #<Metabolite:0x00007fece848d6e0>

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 #<Metabolite:0x00007fece848d6e0>

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 #<Metabolite:0x00007fece848d6e0>

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 #<Metabolite:0x00007fece848d6e0>

OC[C@H]1OC(=O)[C@@H](O)[C@@H]1O
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INCHI for #<Metabolite:0x00007fece848d6e0>

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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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
Molecular FormulaC5H8O5
Average Mass148.114
Monoisotopic Mass148.037173366
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