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Showing metabocard for D-Xylulose (HMDB0001644)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-20 22:13:13 UTC
Update Date2021-09-14 15:44:47 UTC
HMDB IDHMDB0001644
Secondary Accession Numbers
  • HMDB0000654
  • HMDB00654
  • HMDB01644
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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001644 (D-Xylulose)

  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 HMDB0001644 (D-Xylulose)

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 HMDB0001644 (D-Xylulose)

  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>
HMDB0001644

> <DATABASE_NAME>
hmdb

> <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 HMDB0001644 (D-Xylulose)

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 HMDB0001644 (D-Xylulose)

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 HMDB0001644 (D-Xylulose)

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 HMDB0001644 (D-Xylulose)

OC[C@@]1(O)OC[C@@H](O)[C@@H]1O
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INCHI for HMDB0001644 (D-Xylulose)

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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View in JSmolView NMR AssignmentsView Stereo Labels
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
Chemical FormulaC5H10O5
Average Molecular Weight150.1299
Monoisotopic Molecular Weight150.05282343
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 Number20750-28-1
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
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Oxolane
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Industrial application
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point15 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Urine
Tissue Locations
  • Fibroblasts
  • Placenta
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified7.5 (5.0-10.0) uMAdolescent (13-18 years old)BothRibose-5-phosphate isomerase deficiency details
Cerebrospinal Fluid (CSF)Detected and Quantified88 - 166 uMAdolescent (13-18 years old)BothRibose-5-Phosphate Isomerase Deficiency details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
UrineDetected and Quantified39 - 52 umol/mmol creatinineAdolescent (13-18 years old)BothRibose-5-Phosphate Isomerase Deficiency details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Bladder cancer		 details
UrineDetected and Quantified444.0599-2220.299 umol/mmol creatinineChildren (1 - 13 years old)BothPentosuria
    • PENTOSURIA IN CHI...
 details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Ribose-5-phosphate isomerase deficiency
  1. Huck JH, Verhoeven NM, Struys EA, Salomons GS, Jakobs C, van der Knaap MS: Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy. Am J Hum Genet. 2004 Apr;74(4):745-51. Epub 2004 Feb 25. [PubMed:14988808 ]
Pentosuria
  1. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
  2. Alfered E. Fischer, Miriam Reiner (1930). PENTOSURIA IN CHILDRENWITH LABORATORY DATA ON FOUR CASES. Am J Dis Child. 1930;40(6):1193–1207. doi:10.1001/archpedi.1930.01940060033003. Am J Dis Child.
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022698
KNApSAcK IDC00019684
Chemspider ID25059226
KEGG Compound IDC00310
BioCyc IDD-XYLULOSE
BiGG IDNot Available
Wikipedia LinkXylulose
METLIN IDNot Available
PubChem Compound12358757
PDB IDXLF
ChEBI ID17140
Food Biomarker OntologyNot Available
VMH IDXYLU_D
MarkerDB IDMDB00000339
Good Scents IDNot Available
References
Synthesis ReferenceTakeuchi, Sonoko; Tonouchi, Naoto; Yokozeki, Kenzo. Production of xylitol or D-xylulose by fermentation of glucose with Gluconobacter, Acetobacter, and Frateuria. Eur. Pat. Appl. (2000), 10 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Huck JH, Roos B, Jakobs C, van der Knaap MS, Verhoeven NM: Evaluation of pentitol metabolism in mammalian tissues provides new insight into disorders of human sugar metabolism. Mol Genet Metab. 2004 Jul;82(3):231-7. [PubMed:15234337 ]
  2. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Enzymes

Enzyme Details
1. Xylulose kinase
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
Not Available
Gene Name:
XYLB
Uniprot ID:
O75191
Molecular weight:
58381.695
Reactions
Adenosine triphosphate + D-Xylulose → ADP + Xylulose 5-phosphatedetails