Showing metabocard for D-Xylonic acid (MMDBc0000524)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:39:43 UTC
Update Date2024-04-30 19:32:47 UTC
Metabolite IDMMDBc0000524
Metabolite Identification
Common NameD-Xylonic acid
DescriptionD-​Xylonic acid belongs to the family of hydroxy fatty acids. These are fatty acids in which the chain bears an hydroxyl group. ​D-​Xylonic acid has been identified in the human placenta (PMID: 32033212 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9234b7e828>


  Mrv1652305052017402D          

 11 10  0  0  0  0            999 V2000
   -3.4819    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1964   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4819    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7674   -0.2008    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7674   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0530    0.2116    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0530    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3385   -0.2008    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3385   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6240    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0903   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  8  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  8  9  1  1  0  0  0
  6  7  1  1  0  0  0
  4  5  1  1  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f9234b7e828>

HMDB0059750
     RDKit          3D
D-Xylonic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -1.1416   -0.4285   -2.2862 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4215    0.2330   -1.2617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7423    1.5691   -1.4115 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4049   -0.4083    0.0556 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7397    0.5254    1.0555 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1367   -1.0981    0.4175 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2512   -2.0375   -0.5346 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0194   -0.2081    0.7194 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7568    0.7702    1.6496 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6317    0.3379   -0.5514 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8289    0.9587   -0.1921 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1795    2.1295   -0.6901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2207   -1.1893    0.1434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6065    0.0216    1.9186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3628   -1.7071    1.3426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5349   -2.4452   -0.9567 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8307   -0.8500    1.1774 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6391    1.6302    1.1673 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9164    1.0219   -1.0084 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9029   -0.5253   -1.1846 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7140    1.7000    0.4303 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  6
  5 14  1  0
  6 15  1  1
  7 16  1  0
  8 17  1  1
  9 18  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f9234b7e828>


  Mrv1652305052017402D          

 11 10  0  0  0  0            999 V2000
   -3.4819    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1964   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4819    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7674   -0.2008    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7674   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0530    0.2116    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0530    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3385   -0.2008    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3385   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6240    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0903   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  8  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  8  9  1  1  0  0  0
  6  7  1  1  0  0  0
  4  5  1  1  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000524

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4-/m1/s1

> <INCHI_KEY>
QXKAIJAYHKCRRA-FLRLBIABSA-N

> <FORMULA>
C5H10O6

> <MOLECULAR_WEIGHT>
166.129

> <EXACT_MASS>
166.047738042

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.327454141408568

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R)-2,3,4,5-tetrahydroxypentanoic acid

> <ALOGPS_LOGP>
-2.48

> <JCHEM_LOGP>
-2.7794093686666668

> <ALOGPS_LOGS>
0.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.768659694136133

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.393139811550542

> <JCHEM_PKA_STRONGEST_BASIC>
-2.974562302797298

> <JCHEM_POLAR_SURFACE_AREA>
118.22000000000001

> <JCHEM_REFRACTIVITY>
32.3085

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.58e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
xylonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f9234b7e828>

HMDB0059750
     RDKit          3D
D-Xylonic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -1.1416   -0.4285   -2.2862 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4215    0.2330   -1.2617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7423    1.5691   -1.4115 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4049   -0.4083    0.0556 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7397    0.5254    1.0555 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1367   -1.0981    0.4175 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2512   -2.0375   -0.5346 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0194   -0.2081    0.7194 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7568    0.7702    1.6496 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6317    0.3379   -0.5514 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8289    0.9587   -0.1921 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1795    2.1295   -0.6901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2207   -1.1893    0.1434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6065    0.0216    1.9186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3628   -1.7071    1.3426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5349   -2.4452   -0.9567 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8307   -0.8500    1.1774 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6391    1.6302    1.1673 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9164    1.0219   -1.0084 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9029   -0.5253   -1.1846 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7140    1.7000    0.4303 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  6
  5 14  1  0
  6 15  1  1
  7 16  1  0
  8 17  1  1
  9 18  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
M  END
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PDB for #<Metabolite:0x00007f9234b7e828>

HEADER    PROTEIN                                 05-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-MAY-20         0                                  
HETATM    1  C   UNK     0      -6.500   0.395   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -7.833  -0.375   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -6.500   1.935   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -5.166  -0.375   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -5.166  -1.915   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -3.832   0.395   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.832   1.935   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.499  -0.375   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.499  -1.915   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.165   0.395   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.169  -0.375   0.000  0.00  0.00           O+0
CONECT    1    4    3    2                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    6    5                                                  
CONECT    5    4                                                            
CONECT    6    4    8    7                                                  
CONECT    7    6                                                            
CONECT    8    6   10    9                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for #<Metabolite:0x00007f9234b7e828>

COMPND    HMDB0059750
HETATM    1  O1  UNL     1      -1.142  -0.428  -2.286  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.421   0.233  -1.262  1.00  0.00           C  
HETATM    3  O2  UNL     1      -1.742   1.569  -1.411  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.405  -0.408   0.056  1.00  0.00           C  
HETATM    5  O3  UNL     1      -1.740   0.525   1.055  1.00  0.00           O  
HETATM    6  C3  UNL     1      -0.137  -1.098   0.417  1.00  0.00           C  
HETATM    7  O4  UNL     1       0.251  -2.037  -0.535  1.00  0.00           O  
HETATM    8  C4  UNL     1       1.019  -0.208   0.719  1.00  0.00           C  
HETATM    9  O5  UNL     1       0.757   0.770   1.650  1.00  0.00           O  
HETATM   10  C5  UNL     1       1.632   0.338  -0.551  1.00  0.00           C  
HETATM   11  O6  UNL     1       2.829   0.959  -0.192  1.00  0.00           O  
HETATM   12  H1  UNL     1      -2.179   2.130  -0.690  1.00  0.00           H  
HETATM   13  H2  UNL     1      -2.221  -1.189   0.143  1.00  0.00           H  
HETATM   14  H3  UNL     1      -1.607   0.022   1.919  1.00  0.00           H  
HETATM   15  H4  UNL     1      -0.363  -1.707   1.343  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.535  -2.445  -0.957  1.00  0.00           H  
HETATM   17  H6  UNL     1       1.831  -0.850   1.177  1.00  0.00           H  
HETATM   18  H7  UNL     1       0.639   1.630   1.167  1.00  0.00           H  
HETATM   19  H8  UNL     1       0.916   1.022  -1.008  1.00  0.00           H  
HETATM   20  H9  UNL     1       1.903  -0.525  -1.185  1.00  0.00           H  
HETATM   21  H10 UNL     1       2.714   1.700   0.430  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   12
CONECT    4    5    6   13
CONECT    5   14
CONECT    6    7    8   15
CONECT    7   16
CONECT    8    9   10   17
CONECT    9   18
CONECT   10   11   19   20
CONECT   11   21
END
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SMILES for #<Metabolite:0x00007f9234b7e828>

OC[C@@H](O)[C@H](O)[C@@H](O)C(O)=O
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INCHI for #<Metabolite:0x00007f9234b7e828>

InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4-/m1/s1
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Synonyms
ValueSource
D-XylonateChEBI
​D-​xylonateHMDB
L-Xylonic acidHMDB
Xylonic acidHMDB
2,3,4,5-Tetrahydroxypentanoic acidHMDB
XylonateHMDB
D-Xylonic acidGenerator
Molecular FormulaC5H10O6
Average Mass166.129
Monoisotopic Mass166.047738042
IUPAC Name(2R,3S,4R)-2,3,4,5-tetrahydroxypentanoic acid
Traditional Namexylonic acid
CAS Registry NumberNot Available
SMILES
OC[C@@H](O)[C@H](O)[C@@H](O)C(O)=O
InChI Identifier
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4-/m1/s1
InChI KeyQXKAIJAYHKCRRA-FLRLBIABSA-N