Showing metabocard for D-Xylulose (MMDBc0000531)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:39:53 UTC
Update Date2024-04-30 19:32:49 UTC
Metabolite IDMMDBc0000531
Metabolite Identification
Common NameD-Xylulose
DescriptionD-Xylulose (CAS: 551-84-8) is a monosaccharide containing five carbon atoms. D-Xylulose is converted from xylitol by the enzyme NAD+-linked xylitol dehydrogenase (EC 1.1.1.9) in the glucuronate pathway, the most important xylitol-handling metabolic pathway in mammals. This activity has been described in human erythrocytes. Most likely, D-xylulose (as well as D-arabinose or D-ribulose) is a precursor of the pentiol D-arabitol, since pentitols are derived from their corresponding pentose phosphate precursors via pentoses. This pathway can play a role in inherited metabolic disorders underlying the accumulation of pentitols (e.g. ribose 5-phosphate isomerase deficiency and transaldolase deficiency). Although pentitols are present in all living organisms, knowledge concerning their metabolism is limited (PMID:15234337 , Mol Genet Metab. 2004 Jul;82(3):231-7.).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb73ac0e58>


  Mrv1652309042000242D          

 10 10  0  0  0  0            999 V2000
10000.779010000.8748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.494010000.4635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.6963 9999.9316    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.2705 9999.0121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.4758 9999.0204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.389710000.9566    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.722310000.4716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9772 9999.6870    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.8022 9999.6870    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.057110000.4716    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6 10  1  0  0  0  0
  1 10  1  0  0  0  0
 10  3  1  1  0  0  0
  9  4  1  1  0  0  0
  8  5  1  6  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007fdb73ac0e58>

HMDB0001644
     RDKit          3D
D-Xylulose
 20 20  0  0  0  0  0  0  0  0999 V2000
    2.9713   -0.0526   -0.4250 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9469    0.0281    0.5154 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6495    0.1370   -0.2455 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6401    1.2693   -1.0537 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3866   -0.9790   -1.0008 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9840   -1.1295   -1.1070 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6405   -0.0384   -0.3269 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8267   -0.3710    0.2547 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5399    0.2572    0.7005 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6597    1.5184    1.2255 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1815   -0.9628   -0.6984 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1256    0.8697    1.1816 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9380   -0.9553    1.0491 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2031    2.0330   -0.5652 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3397   -1.1303   -2.1534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2197   -2.1384   -0.6552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7356    0.8461   -0.9791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8081   -0.4571    1.2362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5088   -0.5529    1.4598 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2201    1.8085    1.5874 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  6
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  3  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  4 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  6
  8 18  1  0
  9 19  1  1
 10 20  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007fdb73ac0e58>


  Mrv1652309042000242D          

 10 10  0  0  0  0            999 V2000
10000.779010000.8748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.494010000.4635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.6963 9999.9316    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.2705 9999.0121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.4758 9999.0204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.389710000.9566    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.722310000.4716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9772 9999.6870    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.8022 9999.6870    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.057110000.4716    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6 10  1  0  0  0  0
  1 10  1  0  0  0  0
 10  3  1  1  0  0  0
  9  4  1  1  0  0  0
  8  5  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000531

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-2-5(9)4(8)3(7)1-10-5/h3-4,6-9H,1-2H2/t3-,4+,5-/m1/s1

> <INCHI_KEY>
LQXVFWRQNMEDEE-MROZADKFSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.546563401703319

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R)-2-(hydroxymethyl)oxolane-2,3,4-triol

> <ALOGPS_LOGP>
-2.20

> <JCHEM_LOGP>
-2.1276643760000002

> <ALOGPS_LOGS>
0.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.844123223152558

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.292639879315793

> <JCHEM_PKA_STRONGEST_BASIC>
-3.450695969467499

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
30.398299999999992

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.31e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4R)-2-(hydroxymethyl)oxolane-2,3,4-triol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007fdb73ac0e58>

HMDB0001644
     RDKit          3D
D-Xylulose
 20 20  0  0  0  0  0  0  0  0999 V2000
    2.9713   -0.0526   -0.4250 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9469    0.0281    0.5154 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6495    0.1370   -0.2455 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6401    1.2693   -1.0537 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3866   -0.9790   -1.0008 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9840   -1.1295   -1.1070 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6405   -0.0384   -0.3269 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8267   -0.3710    0.2547 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5399    0.2572    0.7005 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6597    1.5184    1.2255 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1815   -0.9628   -0.6984 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1256    0.8697    1.1816 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9380   -0.9553    1.0491 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2031    2.0330   -0.5652 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3397   -1.1303   -2.1534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2197   -2.1384   -0.6552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7356    0.8461   -0.9791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8081   -0.4571    1.2362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5088   -0.5529    1.4598 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2201    1.8085    1.5874 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  6
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  3  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  4 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  6
  8 18  1  0
  9 19  1  1
 10 20  1  0
M  END
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PDB for #<Metabolite:0x00007fdb73ac0e58>

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0    8668.1218668.300   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8669.4558667.532   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8667.9668666.539   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8667.1728664.823   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8663.8218664.838   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8665.5278668.452   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8664.2828667.547   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8664.7578666.082   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8666.2978666.082   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8666.7738667.547   0.000  0.00  0.00           C+0
CONECT    1    2   10                                                       
CONECT    2    1                                                            
CONECT    3   10                                                            
CONECT    4    9                                                            
CONECT    5    8                                                            
CONECT    6    7   10                                                       
CONECT    7    8    6                                                       
CONECT    8    7    9    5                                                  
CONECT    9    8   10    4                                                  
CONECT   10    9    6    1    3                                             
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for #<Metabolite:0x00007fdb73ac0e58>

COMPND    HMDB0001644
HETATM    1  O1  UNL     1       2.971  -0.053  -0.425  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.947   0.028   0.515  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.649   0.137  -0.245  1.00  0.00           C  
HETATM    4  O2  UNL     1       0.640   1.269  -1.054  1.00  0.00           O  
HETATM    5  O3  UNL     1       0.387  -0.979  -1.001  1.00  0.00           O  
HETATM    6  C3  UNL     1      -0.984  -1.129  -1.107  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.641  -0.038  -0.327  1.00  0.00           C  
HETATM    8  O4  UNL     1      -2.827  -0.371   0.255  1.00  0.00           O  
HETATM    9  C5  UNL     1      -0.540   0.257   0.700  1.00  0.00           C  
HETATM   10  O5  UNL     1      -0.660   1.518   1.226  1.00  0.00           O  
HETATM   11  H1  UNL     1       3.182  -0.963  -0.698  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.126   0.870   1.182  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.938  -0.955   1.049  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.203   2.033  -0.565  1.00  0.00           H  
HETATM   15  H5  UNL     1      -1.340  -1.130  -2.153  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.220  -2.138  -0.655  1.00  0.00           H  
HETATM   17  H7  UNL     1      -1.736   0.846  -0.979  1.00  0.00           H  
HETATM   18  H8  UNL     1      -2.808  -0.457   1.236  1.00  0.00           H  
HETATM   19  H9  UNL     1      -0.509  -0.553   1.460  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.220   1.809   1.587  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3   12   13
CONECT    3    4    5    9
CONECT    4   14
CONECT    5    6
CONECT    6    7   15   16
CONECT    7    8    9   17
CONECT    8   18
CONECT    9   10   19
CONECT   10   20
END
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SMILES for #<Metabolite:0x00007fdb73ac0e58>

OC[C@@]1(O)OC[C@@H](O)[C@@H]1O
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INCHI for #<Metabolite:0x00007fdb73ac0e58>

InChI=1S/C5H10O5/c6-2-5(9)4(8)3(7)1-10-5/h3-4,6-9H,1-2H2/t3-,4+,5-/m1/s1
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Synonyms
ValueSource
b-D-XylulofuranoseHMDB
Β-D-xylulofuranoseHMDB
D-LyxuloseHMDB
D-Threo-2-pentuloseHMDB
D-Threo-pentuloseHMDB
XyluloseHMDB
beta-D-Threo-2-pentulofuranoseHMDB
beta-D-Threo-pentulofuranoseHMDB
Β-D-threo-2-pentulofuranoseHMDB
Β-D-threo-pentulofuranoseHMDB
D-XyluloseHMDB
Molecular FormulaC5H10O5
Average Mass150.1299
Monoisotopic Mass150.05282343
IUPAC Name(2R,3S,4R)-2-(hydroxymethyl)oxolane-2,3,4-triol
Traditional Name(2R,3S,4R)-2-(hydroxymethyl)oxolane-2,3,4-triol
CAS Registry NumberNot Available
SMILES
OC[C@@]1(O)OC[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-2-5(9)4(8)3(7)1-10-5/h3-4,6-9H,1-2H2/t3-,4+,5-/m1/s1
InChI KeyLQXVFWRQNMEDEE-MROZADKFSA-N