MiMeDB: Showing metabocard for L-Xylulose 5-phosphate (MMDBc0030076)

Microbial

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:52:59 UTC

Update Date

2022-08-31 17:39:32 UTC

Metabolite ID

MMDBc0030076

Metabolite Identification

Common Name

L-Xylulose 5-phosphate

Description

)Xylulose 5-phosphate (Xu-5-P) is a metabolite of the hexose monophosphate pathway that activates protein phosphatase 2A to mediate the acute effects of carbohydrate feeding on the glycolytic pathway, as well as the coordinate long-term control of the enzymes required for fatty acid and triglyceride synthesis. Xu-5-P is the signal for the coordinated control of lipogenesis. Feeding carbohydrate causes levels of glucose, Glucose-6-phosphate (Glc-6-P), and Fructose-6-phosphate (Fru-6-P) to rise. Elevation of Fru-6-P leads to elevation of Xu-5-P in reactions catalyzed by the near-equilibrium isomerases of the nonoxidative portion of the hexose monophosphate pathway (ribulose 5-phosphate (Ru5P) epimerase [EC 5.1.3.1], ribose 5-phosphate (Rib5P) isomerase [EC 5.3.1.6], transaldolase [EC 2.2.1.2], and transketolase [EC 2.2.1.1]). The elevation of Xu-5-P is the coordinating signal that both acutely activates phosphofructokinase [PFK

Structure

MOL SDF PDB SMILES InChI


  Mrv1533005191517142D          

 14 13  0  0  0  0            999 V2000
   -3.4528   -0.2301    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7383    0.1823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0239   -0.2301    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3094    0.1823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5949   -0.2301    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1195    0.1823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8339   -0.2301    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5484    0.1823    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.2629   -0.2301    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.0239   -1.0551    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3094    1.0073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5949   -1.0551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5302    0.9373    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5891   -0.7105    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  2  1  0  0  0  0
  3 10  2  0  0  0  0
  4 11  1  0  0  0  0
  5 12  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 14  1  0  0  0  0
  8 13  2  0  0  0  0
M  CHG  2   9  -1  14  -1
M  END
> <DATABASE_ID>
MMDBc0030076

> <DATABASE_NAME>
MIME

> <SMILES>
CC(COP([O-])([O-])=O)C(C)C(=O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C7H15O6P/c1-5(4-13-14(10,11)12)6(2)7(9)3-8/h5-6,8H,3-4H2,1-2H3,(H2,10,11,12)/p-2

> <INCHI_KEY>
GOBYCGYLQSIFMQ-UHFFFAOYSA-L

> <FORMULA>
C7H13O6P

> <MOLECULAR_WEIGHT>
224.15

> <EXACT_MASS>
224.046072296

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
19.621614730032192

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-hydroxy-3,4-dimethyl-5-(phosphonatooxy)pentan-2-one

> <ALOGPS_LOGP>
-0.42

> <JCHEM_LOGP>
-0.21814926899999965

> <ALOGPS_LOGS>
-0.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.835889778956463

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8124696570931116

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2949765686081074

> <JCHEM_POLAR_SURFACE_AREA>
109.72

> <JCHEM_REFRACTIVITY>
46.7292

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.85e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-hydroxy-3,4-dimethyl-5-(phosphonatooxy)pentan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-MAY-15         0                                  
HETATM    1  O   UNK     0      -6.445  -0.430   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -5.111   0.340   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.778  -0.430   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.444   0.340   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.110  -0.430   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.223   0.340   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.557  -0.430   0.000  0.00  0.00           O+0
HETATM    8  P   UNK     0       2.890   0.340   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0       4.224  -0.430   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0      -3.778  -1.970   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.444   1.880   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.110  -1.970   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.856   1.750   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       2.966  -1.326   0.000  0.00  0.00           O-1
CONECT    1    2                                                            
CONECT    2    3    1                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6   12                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   14   13                                             
CONECT    9    8                                                            
CONECT   10    3                                                            
CONECT   11    4                                                            
CONECT   12    5                                                            
CONECT   13    8                                                            
CONECT   14    8                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
L-Xylulose -5-phosphoric acid	Generator

Molecular Formula

C₇H₁₃O₆P

Average Mass

224.15

Monoisotopic Mass

224.046072296

IUPAC Name

1-hydroxy-3,4-dimethyl-5-(phosphonatooxy)pentan-2-one

Traditional Name

1-hydroxy-3,4-dimethyl-5-(phosphonatooxy)pentan-2-one

CAS Registry Number

60802-29-1

SMILES

CC(COP([O-])([O-])=O)C(C)C(=O)CO

InChI Identifier

InChI=1S/C7H15O6P/c1-5(4-13-14(10,11)12)6(2)7(9)3-8/h5-6,8H,3-4H2,1-2H3,(H2,10,11,12)/p-2

InChI Key

GOBYCGYLQSIFMQ-UHFFFAOYSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alkyl phosphates. These are organic compounds containing a phosphate group that is linked to one or more alkyl chains.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Organic phosphoric acids and derivatives

Sub Class

Phosphate esters

Direct Parent

Alkyl phosphates

Alternative Parents

Substituents

Alkyl phosphate
Alpha-hydroxy ketone
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Organic anion
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	38.5 g/L	ALOGPS
logP	-0.42	ALOGPS
logP	-0.22	ChemAxon
logS	-0.83	ALOGPS
pKa (Strongest Acidic)	1.81	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	109.72 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	46.73 m³·mol⁻¹	ChemAxon
Polarizability	19.62 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	207.1
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	86.3
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	309.9
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	459.2
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	365.3
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	284.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	1412.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	86.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	567.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	259.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	193.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	164.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	87.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	285.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	378.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	59.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	263.8
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	968.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	684.1

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

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

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018153	3-Keto-L-gulonate 6-phosphate	L-Xylulose 5-phosphate	3-keto-L-gulonate-6-phosphate decarboxylase SgbH	Carboxylation	PathBank	31602464
MMDBr0018154	L-Xylulose 5-phosphate	L-ribulose 5-phosphate	L-ribulose-5-phosphate 3-epimerase UlaE	Epimerization	PathBank	31602464
MMDBr0018155	3-Keto-L-gulonate 6-phosphate	L-Xylulose 5-phosphate	3-keto-L-gulonate-6-phosphate decarboxylase UlaD	Carboxylation	PathBank	31602464
MMDBr0019367	L-Xylulose	L-Xylulose 5-phosphate	L-xylulose/3-keto-L-gulonate kinase	Phosphorylation	PathBank	31602464
MMDBr0019368	L-Xylulose 5-phosphate	L-ribulose 5-phosphate	Putative L-ribulose-5-phosphate 3-epimerase SgbU	Epimerization	PathBank	31602464

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	3	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Chicken	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	340	Human feces; Human pleural fluid plaque; Pig ; Human ; Human subgingival plaque; Cattle ; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	197	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Chicken	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	98	Human feces; Human ; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	114	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	5	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	1	Human feces	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for L-Xylulose 5-phosphate (MMDBc0030076)

MOL for #<Metabolite:0x00007fae018a8228>

3D MOL for #<Metabolite:0x00007fae018a8228>

3D SDF for #<Metabolite:0x00007fae018a8228>

3D-SDF for #<Metabolite:0x00007fae018a8228>

PDB for #<Metabolite:0x00007fae018a8228>

3D PDB for #<Metabolite:0x00007fae018a8228>

SMILES for #<Metabolite:0x00007fae018a8228>

INCHI for #<Metabolite:0x00007fae018a8228>

Structure for #<Metabolite:0x00007fae018a8228>

3D Structure for #<Metabolite:0x00007fae018a8228>