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 Date2025-01-15 22:25:56 UTC
Metabolite IDMMDBc0048868
Metabolite Identification
Common NameD-Xylono-1,5-lactone
DescriptionD-xylonolactone is a lactone derivative of xylonic acid. It is an intermediate in the pentose and glucuronate interconversion pathway and can be formed from either D-xylonic acid or D-xylose. D-xylose is a simple 5 carbon sugar that is found in a variety of edible plants. It is also frequently used in intestinal absorption tests to help diagnose problems that prevent the small intestine from absorbing nutrients in food. Xylose is also the first saccharide added to the serine or threonine in the proteoglycan type O-glycosylation and so it is the first saccharide in biosynthetic pathways of most anionic polysaccharides such as heparan sulfate and chondroitin sulfate. D-xylose is normally easily absorbed by the intestines where it can be converted to D-xylonolactone by intestinal D-xylose 1-dehydrogenase (EC 1.1.1.175).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f922ddf6120>


  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
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3D MOL for #<Metabolite:0x00007f922ddf6120>

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
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3D SDF for #<Metabolite:0x00007f922ddf6120>


  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

$$$$
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3D-SDF for #<Metabolite:0x00007f922ddf6120>

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
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PDB for #<Metabolite:0x00007f922ddf6120>

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
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3D PDB for #<Metabolite:0x00007f922ddf6120>

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
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SMILES for #<Metabolite:0x00007f922ddf6120>

O[C@@H]1COC(=O)[C@H](O)[C@H]1O
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INCHI for #<Metabolite:0x00007f922ddf6120>

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