MiMeDB: Showing metabocard for D-Xylulose 1-phosphate (MMDBc0047953)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-23 23:18:36 UTC

Update Date

2022-09-01 02:13:05 UTC

Metabolite ID

MMDBc0047953

Metabolite Identification

Common Name

D-Xylulose 1-phosphate

Description

D-Xylulose 1-phosphate is produced in the hepatocytes and is the product of fructokinase (ketohexokinase, EC 2.7.1.3) phosphorylation of D-xylulose. The cleavage of D-xylulose-1-phosphate glycolaldehyde by aldolase (fructose-bisphosphate aldolase, EC 4.1.2.13) produces glycolaldehyde which is an oxalate precursor. The distribution of both enzymes in human tissues indicates that this reaction sequence occurs mainly in the liver, to a lesser extent in the kidney, and very little in heart, brain and muscle. The kinetic properties of fructokinase show that this enzyme can phosphorylate D-xylulose as readily as D-fructose (PMID: 6458298 , 13898172 , 6284103 , 2996495 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652304092018262D          

 14 13  0  0  0  0            999 V2000
 9988.6266 9988.1094    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9987.9129 9987.6974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.3422 9987.6974    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9988.6266 9988.9344    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9987.1986 9988.1094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9987.9129 9986.8724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.0578 9988.1094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.3422 9986.8724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9986.4842 9987.6974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.7735 9987.6974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.7697 9988.1094    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9986.1832 9988.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.0533 9987.6955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.3583 9988.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  1  0  0  0
  5  9  1  0  0  0  0
  7 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0047953

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3,5-7,9H,1-2H2,(H2,10,11,12)/t3-,5+/m1/s1

> <INCHI_KEY>
NBOCCPQHBPGYCX-WUJLRWPWSA-N

> <FORMULA>
C5H11O8P

> <MOLECULAR_WEIGHT>
230.109

> <EXACT_MASS>
230.019154312

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
18.009626265060398

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(3S,4R)-3,4,5-trihydroxy-2-oxopentyl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-1.80

> <JCHEM_LOGP>
-2.7602629813333333

> <ALOGPS_LOGS>
-0.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.208722028772268

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.178619064267565

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9797461037901494

> <JCHEM_POLAR_SURFACE_AREA>
144.52

> <JCHEM_REFRACTIVITY>
42.472199999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.47e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3S,4R)-3,4,5-trihydroxy-2-oxopentyl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-APR-20         0                                  
HETATM    1  C   UNK     0    8645.4368644.471   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8644.1048643.702   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8646.7728643.702   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8645.4368646.011   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8642.7718644.471   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    8644.1048642.162   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8648.1088644.471   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0    8646.7728642.162   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8641.4378643.702   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8649.4448643.702   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0    8640.1048644.471   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0    8640.8758645.807   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8638.7668643.698   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0    8639.3368645.807   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1                                                            
CONECT    5    2    9                                                       
CONECT    6    2                                                            
CONECT    7    3   10                                                       
CONECT    8    3                                                            
CONECT    9    5   11                                                       
CONECT   10    7                                                            
CONECT   11    9   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
D-Xylulose 1-phosphoric acid	Generator
L-Threo-pentulose 1-phosphate	HMDB
Xylulose-1-phosphate	HMDB
D-Xylulose-1-phosphate	HMDB
D-Xylulose 1-phosphate	HMDB

Molecular Formula

C₅H₁₁O₈P

Average Mass

230.109

Monoisotopic Mass

230.019154312

IUPAC Name

{[(3S,4R)-3,4,5-trihydroxy-2-oxopentyl]oxy}phosphonic acid

Traditional Name

[(3S,4R)-3,4,5-trihydroxy-2-oxopentyl]oxyphosphonic acid

CAS Registry Number

63323-91-1

SMILES

OC[C@@H](O)[C@H](O)C(=O)COP(O)(O)=O

InChI Identifier

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3,5-7,9H,1-2H2,(H2,10,11,12)/t3-,5+/m1/s1

InChI Key

NBOCCPQHBPGYCX-WUJLRWPWSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Glycerone phosphate
Pentose monosaccharide
Monosaccharide phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Beta-hydroxy ketone
Acyloin
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Polyol
Organic oxide
Hydrocarbon derivative
Primary alcohol
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	24.7 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.8	ChemAxon
logS	-0.97	ALOGPS
pKa (Strongest Acidic)	1.18	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	144.52 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	42.47 m³·mol⁻¹	ChemAxon
Polarizability	18.01 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002b-9100000000-b93fc0dc722f1a856d51	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-4cacfe194df5a6da8380	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-003r-9760000000-0adb9dbb1f8e7e03f4cd	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00r2-9400000000-36d669725440691a6e87	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-9000000000-e449887e5d2026ea1f5f	2021-09-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0192803	Ketohexokinase	Enzyme	P50053	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0001206	D-Xylulose 1-phosphate	Dihydroxyacetone phosphate	Not Available	D-Fructose 1-Phosphate D-Glyceraldehyde-3-Phosphate-Lyase	VMH	2996495 6284103 6298387
MMDBr0001527	Adenosine triphosphate	ADP	Not Available	Ketohexokinase (D-Xylulose)	VMH	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	8	Human feces; Human sputum	Metabolic reconstruction
Bacteria	Bacteroidetes	2	Human feces	Metabolic reconstruction
Bacteria	Actinobacteria	5	Human feces; Human	Metabolic reconstruction
Bacteria	Firmicutes	2	Human feces; Human	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0006534

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023963

KNApSAcK ID

Not Available

Chemspider ID

133112

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

151020

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bais R, James HM, Rofe AM, Conyers RA: The purification and properties of human liver ketohexokinase. A role for ketohexokinase and fructose-bisphosphate aldolase in the metabolic production of oxalate from xylitol. Biochem J. 1985 Aug 15;230(1):53-60. doi: 10.1042/bj2300053. [PubMed:2996495 ]
James HM, Bais R, Edwards JB, Rofe AM, Conyers AJ: Models for the metabolic production of oxalate from xylitol in humans: a role for fructokinase and aldolase. Aust J Exp Biol Med Sci. 1982 Feb;60(Pt 1):117-22. doi: 10.1038/icb.1982.11. [PubMed:6284103 ]
Barngrover DA, Stevens HC, Dills WL Jr: D-Xylulose-1-phosphate: enzymatic assay and production in isolated rat hepatocytes. Biochem Biophys Res Commun. 1981 Sep 16;102(1):75-80. doi: 10.1016/0006-291x(81)91490-x. [PubMed:6458298 ]
GHALAMBOR MA, HEATH EC: The metabolism of L-fucose. II. The enzymatic cleavage of L-fuculose 1-phosphate. J Biol Chem. 1962 Aug;237:2427-33. [PubMed:13898172 ]

Showing metabocard for D-Xylulose 1-phosphate (MMDBc0047953)

MOL for #<Metabolite:0x000055d24a34a130>

3D MOL for #<Metabolite:0x000055d24a34a130>

3D SDF for #<Metabolite:0x000055d24a34a130>

3D-SDF for #<Metabolite:0x000055d24a34a130>

PDB for #<Metabolite:0x000055d24a34a130>

3D PDB for #<Metabolite:0x000055d24a34a130>

SMILES for #<Metabolite:0x000055d24a34a130>

INCHI for #<Metabolite:0x000055d24a34a130>

Structure for #<Metabolite:0x000055d24a34a130>

3D Structure for #<Metabolite:0x000055d24a34a130>