aldehydo-D-Xylose (YMDB00779)

You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

Identification

YMDB ID

YMDB00779

Name

aldehydo-D-Xylose

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

D-Xylose, also known as xylose or xylopyranose, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-Xylose is an extremely weak basic (essentially neutral) compound (based on its pKa). D-Xylose exists in all living species, ranging from bacteria to humans. D-xylose can be converted into D-xylitol through the action of the enzyme trifunctional aldehyde reductase/xylose reductase/glucose 1-dehydrogenase (nadp(+)). In yeast, D-xylose is involved in the metabolic pathway called the xylitol degradation pathway. D-Xylose is a potentially toxic compound.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

(+)-Xylose
(D)-Xylose
aldehydo-D-xylose
D-(+)-xylose
D-Xyl
D-xylo-pentose
d-Xylose
Pentose
wood sugar
Xylo-pfan
Xylomed
Xylose
Xylose, d-
Xyloside
(3R,4S,5R)-Tetrahydro-2H-pyran-2,3,4,5-tetrol
D-Xylopentose
Xylopyranose
D Xylose
D-Xylopyranose

CAS number

58-86-6

Weight

Average: 150.1299
Monoisotopic: 150.05282343

InChI Key

PYMYPHUHKUWMLA-VPENINKCSA-N

InChI

InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4+,5+/m0/s1

IUPAC Name

(3R,4S,5R)-oxane-2,3,4,5-tetrol

Traditional IUPAC Name

d-xylose

Chemical Formula

C₅H₁₀O₅

SMILES

[H][C@@](O)(CO)[C@]([H])(O)[C@@]([H])(O)C=O

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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Oxane
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-xylose (CHEBI:53455 )
Aldoses (C00181 )

Physical Properties

State

Solid

Charge

Melting point

90.5 °C

Experimental Properties

Property	Value	Reference
Water Solubility	555 mg/mL [MERCK INDEX (1996)]	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	1220 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-2.3	ChemAxon
logS	0.91	ALOGPS
pKa (Strongest Acidic)	11.31	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	29.96 m³·mol⁻¹	ChemAxon
Polarizability	13.43 Å³	ChemAxon
Number of Rings	1	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

extracellular
cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Amino sugar and nucleotide sugar metabolism	PW002413
Starch and sucrose metabolism	PW002481
xylitol degradation	PW002433

KEGG Pathways

Amino sugar and nucleotide sugar metabolism	ec00520
Pentose and glucuronate interconversions	ec00040
Starch and sucrose metabolism	ec00500

SMPDB Reactions

aldehydo-D-Xylose + NADP → D-Xylitol + NADPH + hydron

KEGG Reactions

aldehydo-D-Xylose + NADPH + hydron → NADP + Xylitol

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0920000000-53943f97f7f99da85d3b	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0uxr-0920000000-c093331f073f56253951	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0920000000-53943f97f7f99da85d3b	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0uxr-0920000000-c093331f073f56253951	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-000x-9400000000-f20d1c35a7eeea1609a5	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-00g0-9256300000-ae2d57025e3828494249	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_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_3_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0udi-2900000000-5a95e26ce7a03eeb4a1c	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00kr-9200000000-ffce45222cab00a0c302	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0udr-5900000000-8d1e329345725c7495d0	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0c09-9300000000-68bb5f7897018aa0f358	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0a4i-9000000000-f76bfc808747fe9aad84	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-9000000000-a7b4fd29d3979cb7bf06	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0a4i-9100000000-509fbbf4a256fe9f3700	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0udi-9200000000-7c094cf44853525b1af6	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-9000000000-b22a8f9c232e806e5c66	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0ue9-0900000000-4856e933b915ddbb0554	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0f89-0900000000-79e8278d7ae6b34a7772	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-08os-9100000000-64c106194d5825a11d36	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-1900000000-988a7d2dad8bc555d502	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000t-2900000000-31127350481e63c82ff7	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-264c06bc93b8e518bbfb	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0gc0-1900000000-e784a3fdca89dcb59c12	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0m4p-9100000000-fc295e2732f55a0a18c1	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0007-9000000000-ba5f29c2c79df8d0956f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-7900000000-524214992b29f1ff9b80	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-9000000000-f758a7d33dac04b06275	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-4b3e154b12c2ee07bf58	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C 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
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	JSpectraViewer

References

References:

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
Senac, T., Hahn-Hagerdal, B. (1990). "Intermediary Metabolite Concentrations in Xylulose- and Glucose-Fermenting Saccharomyces cerevisiae Cells." Appl Environ Microbiol 56:120-126.16348083

Synthesis Reference:

Lavarack, B. P.; Griffin, G.; Rodman, D. Optimizing the autohydrolysis of bagasse to extract D-xylose. Proceedings of the Conference of the Australian Society of Sugar Cane Technologists (1999), 21st 394-400.

External Links:

Resource	Link
CHEBI ID	15936
HMDB ID	HMDB00098
Pubchem Compound ID	644160
Kegg ID	C00181
ChemSpider ID	119104
FOODB ID	FDB005944
Wikipedia	Xylose
BioCyc ID	XYLOSE

Enzymes

Protein Details

1. NADPH-dependent aldose reductase GRE3

General function:: Involved in oxidoreductase activity
Specific function:: Reduces the cytotoxic compound methylglyoxal (MG) to (R)-lactaldehyde similar to GRE2. MG is synthesized via a bypath of glycolysis from dihydroxyacetone phosphate and is believed to play a role in cell cycle regulation and stress adaptation. In pentose-fermenting yeasts, aldose reductase catalyzes the reduction of xylose into xylitol. The purified enzyme catalyzes this reaction, but the inability of S.cerevisiae to grow on xylose as sole carbon source indicates that the physiological function is more likely methylglyoxal reduction
Gene Name:: GRE3
Uniprot ID:: P38715
Molecular weight:: 37118.5

Reactions

Alditol + NAD(P)(+) → aldose + NAD(P)H.
(R)-lactaldehyde + NADP(+) → methylglyoxal + NADPH.

Structure for #<Compound:0xa420bc4c>

Enzymes

Reactions