Xylulose 5-phosphate (YMDB00362)

Identification

YMDB ID

YMDB00362

Name

Xylulose 5-phosphate

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Xylulose 5-phosphate belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups. Xylulose 5-phosphate exists in all living species, ranging from bacteria to plants to humans. In yeast, xylulose 5-phosphate is involved in the metabolic pathway called the xylitol degradation pathway. Based on a literature review a significant number of articles have been published on Xylulose 5-phosphate.

Structure

MOL SDF PDB SMILES InChI

Synonyms

D-xylulose 5-phosphate
D-xylulose 5-PO4
D-xylulose-5-P
D-xylulose-5-phosphate
Xu-5-P
Xylulose 5-phosphate
Xylulose 5-phosphic acid
xylulose-P
Xylulose-phosphate
5-O-Phosphono-D-threo-pentos-2-ulose
5-O-Phosphono-D-xylulose
D-Xylulose-5-phosphoric acid
Xylulose 5-phosphoric acid
Xylulose-5-phosphate
Xylulose-5-phosphate, (D)-isomer
keto-D-Xylulose 5-phosphate

CAS number

4212-65-1

Weight

Average: 230.1098
Monoisotopic: 230.01915384

InChI Key

FNZLKVNUWIIPSJ-RFZPGFLSSA-N

InChI

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5-/m1/s1

IUPAC Name

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

Traditional IUPAC Name

ribulose-5-phosphate

Chemical Formula

C₅H₁₁O₈P

SMILES

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

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
Monosaccharide phosphate
Monoalkyl phosphate
Acyloin
Beta-hydroxy ketone
Organic phosphoric acid derivative
Alkyl phosphate
Phosphoric acid ester
Alpha-hydroxy ketone
Ketone
Secondary alcohol
Polyol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alcohol
Primary alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

xylulose 5-phosphate (CHEBI:16332 )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	26.1 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.8	ChemAxon
logS	-0.95	ALOGPS
pKa (Strongest Acidic)	1.48	ChemAxon
pKa (Strongest Basic)	-3.3	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	18.05 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Riboneogenesis	PW002511
xylitol degradation	PW002433

KEGG Pathways

Methane metabolism	ec00680
Pentose and glucuronate interconversions	ec00040
Pentose phosphate pathway	ec00030

SMPDB Reactions

D-Xylulose + Adenosine triphosphate → Xylulose 5-phosphate + ADP + hydron

Xylulose 5-phosphate → L-ribulose 5-phosphate

Xylulose 5-phosphate → D-ribulose 5-phosphate

Xylulose 5-phosphate ↔ D-ribulose 5-phosphate

Xylulose 5-phosphate + D-Ribose 5-phosphate → L-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate

KEGG Reactions

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0592-9800000000-d336b0e2eff1402939d8	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0a4i-9023200000-1dd7d8e1f64921beb234	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - QTOF 4V, negative	splash10-004j-9170000000-997b74cb48ace33cccd6	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 23V, negative	splash10-004j-9000000000-6bc02f4fe0074c9abd68	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 25V, negative	splash10-004j-9000000000-bdadc167eb24a88aac33	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 27V, negative	splash10-004j-9000000000-93d31d83892e88720b87	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 30V, negative	splash10-004i-9000000000-10cd88e85162e6269751	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 33V, negative	splash10-004i-9000000000-e9f2bf02f0d01a879d20	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 35V, negative	splash10-004i-9000000000-732cd41f406b617c64a0	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 40V, negative	splash10-004i-9000000000-25a5607c50f3e9bb5a14	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 45V, negative	splash10-004i-9000000000-ea506b9429ed926c5f93	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 23V, negative	splash10-0002-9120000000-1172898b831a36b0afcb	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 25V, negative	splash10-0002-9110000000-132340cd62e8e4a0ccd2	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 27V, negative	splash10-0002-9110000000-297d4c6907686258e552	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 30V, negative	splash10-0002-9100000000-1cce49f995c912b1cc94	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 33V, negative	splash10-0002-9100000000-8bba2d7511cc9829eb36	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 35V, negative	splash10-0002-9100000000-89b3b4fdcb0326bfa0e0	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 40V, negative	splash10-0002-9100000000-91e850ff1cd255a2f7fd	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 45V, negative	splash10-002b-9100000000-9c43f84a30add3ebce50	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 16V, negative	splash10-0002-9000000000-75847d481a06c31fa479	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 16V, negative	splash10-004i-0091000000-0af17cfb2eb7eab94967	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01q9-3790000000-6f5913e9948fa7667e41	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0btd-9710000000-3724bb9f611bbdc1fe11	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-8bc9cecb2dddad8ca5e3	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-9520000000-c36fdbcc1d3b19b2fafd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-b67b8ea484aa4ddb40e3	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-82b17cf4f5a8c927fe64	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer

References

References:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Vaseghi, S., Baumeister, A., Rizzi, M., Reuss, M. (1999). "In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae." Metab Eng 1:128-140.10935926
Senac, T., Hahn-Hagerdal, B. (1990). "Intermediary Metabolite Concentrations in Xylulose- and Glucose-Fermenting Saccharomyces cerevisiae Cells." Appl Environ Microbiol 56:120-126.16348083
Bar, J., Naumann, M., Reuter, R., Kopperschlager, G. (1996). "Improved purification of ribulose 5-phosphate 3-epimerase from Saccharomyces cerevisiae and characterization of the enzyme." Bioseparation 6:233-241.9032985

Synthesis Reference:

Shaeri, Jobin; Wohlgemuth, Roland; Woodley, John M. Semiquantitative Process Screening for the Biocatalytic Synthesis of D-Xylulose-5-phosphate. Organic Process Research & Development (2006), 10(3), 605-610.

External Links:

Resource	Link
CHEBI ID	16332
HMDB ID	HMDB00868
Pubchem Compound ID	850
Kegg ID	C00231
ChemSpider ID	388330
FOODB ID	FDB022290
Wikipedia	Xylulose_5-phosphate
BioCyc ID	XYLULOSE-5-PHOSPHATE

Enzymes

Protein Details

1. Transketolase 2

General function:: Involved in catalytic activity
Specific function:: Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate
Gene Name:: TKL2
Uniprot ID:: P33315
Molecular weight:: 75028.79688

Reactions

Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate → D-ribose 5-phosphate + D-xylulose 5-phosphate.

Protein Details

2. Transketolase 1

General function:: Involved in catalytic activity
Specific function:: Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate
Gene Name:: TKL1
Uniprot ID:: P23254
Molecular weight:: 73805.0

Reactions

Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate → D-ribose 5-phosphate + D-xylulose 5-phosphate.

Protein Details

3. Xylulose kinase

General function:: Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:: ATP + D-xylulose = ADP + D-xylulose 5- phosphate
Gene Name:: XKS1
Uniprot ID:: P42826
Molecular weight:: 68320.29688

Reactions

ATP + D-xylulose → ADP + D-xylulose 5-phosphate.

Protein Details

4. Ribulose-phosphate 3-epimerase

General function:: Involved in catalytic activity
Specific function:: Involved in the protective response to oxidative stress
Gene Name:: RPE1
Uniprot ID:: P46969
Molecular weight:: 25966.90039

Reactions

D-ribulose 5-phosphate → D-xylulose 5-phosphate.

Structure for #<Compound:0xaf077754>

Enzymes

Reactions

Reactions

Reactions

Reactions