Showing metabocard for D-Xylono-1,5-lactone (MMDBc0048868)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:12:26 UTC
Update Date2022-09-01 02:15:00 UTC
Metabolite IDMMDBc0048868
Metabolite Identification
Common NameD-Xylono-1,5-lactone
DescriptionD-Xylono-1,5-lactone, also known as D-xylonolactone, belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety. D-Xylono-1,5-lactone has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make D-xylono-1,5-lactone a potential biomarker for the consumption of these foods. D-Xylono-1,5-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-Xylono-1,5-lactone.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560be06a6250>


  Mrv0541 02241201502D          

 10 10  0  0  1  0            999 V2000
    8.9332   -9.3703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6476   -9.7829    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.3621   -9.3703    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.3621   -8.5453    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.6476   -8.1328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6476   -7.3078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9332   -8.5453    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0766   -8.1328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0766   -9.7829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6476  -10.6079    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  2  3  1  0  0  0  0
  2 10  1  6  0  0  0
  3  4  1  0  0  0  0
  3  9  1  1  0  0  0
  4  5  1  0  0  0  0
  4  8  1  6  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x0000560be06a6250>

HMDB0011676
     RDKit          3D
D-Xylono-1,5-lactone
 18 18  0  0  0  0  0  0  0  0999 V2000
   -1.3762    2.6190    0.5069 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7288    1.6733   -0.0120 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5006    1.8384   -0.6374 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5437    0.8971   -0.5527 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9523   -0.5007   -0.6038 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9467   -1.4605   -0.4912 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0829   -0.5869    0.4827 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4583   -1.8618    0.8083 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2658    0.2719    0.0171 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3600    0.1404    0.8324 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0608    1.0138    0.4253 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2410    1.0252   -1.4131 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4863   -0.6060   -1.6140 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6265   -2.3184   -0.1362 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3267   -0.0574    1.3699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8039   -1.8326    1.7549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4838    0.0239   -1.0609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1249   -0.2786    0.3239 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
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  6
  6 14  1  0
  7 15  1  1
  8 16  1  0
  9 17  1  6
 10 18  1  0
M  END
Download

3D SDF for #<Metabolite:0x0000560be06a6250>


  Mrv0541 02241201502D          

 10 10  0  0  1  0            999 V2000
    8.9332   -9.3703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6476   -9.7829    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.3621   -9.3703    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.3621   -8.5453    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.6476   -8.1328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6476   -7.3078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9332   -8.5453    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0766   -8.1328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0766   -9.7829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6476  -10.6079    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  2  3  1  0  0  0  0
  2 10  1  6  0  0  0
  3  4  1  0  0  0  0
  3  9  1  1  0  0  0
  4  5  1  0  0  0  0
  4  8  1  6  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0048868

> <DATABASE_NAME>
MIME

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

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

> <INCHI_KEY>
XXBSUZSONOQQGK-FLRLBIABSA-N

> <FORMULA>
C5H8O5

> <MOLECULAR_WEIGHT>
148.114

> <EXACT_MASS>
148.037173366

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
12.532979098654218

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5R)-3,4,5-trihydroxyoxan-2-one

> <ALOGPS_LOGP>
-2.09

> <JCHEM_LOGP>
-2.114938244

> <ALOGPS_LOGS>
0.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.26573815440348

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.630185047833567

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5403563636526956

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
28.8163

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.30e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-xylonolactone

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x0000560be06a6250>

HMDB0011676
     RDKit          3D
D-Xylono-1,5-lactone
 18 18  0  0  0  0  0  0  0  0999 V2000
   -1.3762    2.6190    0.5069 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7288    1.6733   -0.0120 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5006    1.8384   -0.6374 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5437    0.8971   -0.5527 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9523   -0.5007   -0.6038 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9467   -1.4605   -0.4912 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0829   -0.5869    0.4827 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4583   -1.8618    0.8083 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2658    0.2719    0.0171 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3600    0.1404    0.8324 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0608    1.0138    0.4253 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2410    1.0252   -1.4131 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4863   -0.6060   -1.6140 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6265   -2.3184   -0.1362 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3267   -0.0574    1.3699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8039   -1.8326    1.7549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4838    0.0239   -1.0609 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1249   -0.2786    0.3239 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
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  6
  6 14  1  0
  7 15  1  1
  8 16  1  0
  9 17  1  6
 10 18  1  0
M  END
Download

PDB for #<Metabolite:0x0000560be06a6250>

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  C   UNK     0      16.675 -17.491   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      18.009 -18.261   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      19.343 -17.491   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      19.343 -15.951   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      18.009 -15.181   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      18.009 -13.641   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      16.675 -15.951   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      20.676 -15.181   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      20.676 -18.261   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      18.009 -19.801   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3   10                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    1    5                                                       
CONECT    8    4                                                            
CONECT    9    3                                                            
CONECT   10    2                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
Download

3D PDB for #<Metabolite:0x0000560be06a6250>

COMPND    HMDB0011676
HETATM    1  O1  UNL     1      -1.376   2.619   0.507  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.729   1.673  -0.012  1.00  0.00           C  
HETATM    3  O2  UNL     1       0.501   1.838  -0.637  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.544   0.897  -0.553  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.952  -0.501  -0.604  1.00  0.00           C  
HETATM    6  O3  UNL     1       1.947  -1.461  -0.491  1.00  0.00           O  
HETATM    7  C4  UNL     1      -0.083  -0.587   0.483  1.00  0.00           C  
HETATM    8  O4  UNL     1      -0.458  -1.862   0.808  1.00  0.00           O  
HETATM    9  C5  UNL     1      -1.266   0.272   0.017  1.00  0.00           C  
HETATM   10  O5  UNL     1      -2.360   0.140   0.832  1.00  0.00           O  
HETATM   11  H1  UNL     1       2.061   1.014   0.425  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.241   1.025  -1.413  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.486  -0.606  -1.614  1.00  0.00           H  
HETATM   14  H4  UNL     1       1.626  -2.318  -0.136  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.327  -0.057   1.370  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.804  -1.833   1.755  1.00  0.00           H  
HETATM   17  H7  UNL     1      -1.484   0.024  -1.061  1.00  0.00           H  
HETATM   18  H8  UNL     1      -3.125  -0.279   0.324  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    9
CONECT    3    4
CONECT    4    5   11   12
CONECT    5    6    7   13
CONECT    6   14
CONECT    7    8    9   15
CONECT    8   16
CONECT    9   10   17
CONECT   10   18
END
Download

SMILES for #<Metabolite:0x0000560be06a6250>

O[C@@H]1COC(=O)[C@H](O)[C@H]1O
Download

INCHI for #<Metabolite:0x0000560be06a6250>

InChI=1S/C5H8O5/c6-2-1-10-5(9)4(8)3(2)7/h2-4,6-8H,1H2/t2-,3+,4-/m1/s1
Download
Synonyms
ValueSource
D-XylonolactoneChEBI
XylonolactoneHMDB
Molecular FormulaC5H8O5
Average Mass148.114
Monoisotopic Mass148.037173366
IUPAC Name(3R,4S,5R)-3,4,5-trihydroxyoxan-2-one
Traditional NameD-xylonolactone
CAS Registry NumberNot Available
SMILES
O[C@@H]1COC(=O)[C@H](O)[C@H]1O
InChI Identifier
InChI=1S/C5H8O5/c6-2-1-10-5(9)4(8)3(2)7/h2-4,6-8H,1H2/t2-,3+,4-/m1/s1
InChI KeyXXBSUZSONOQQGK-FLRLBIABSA-N