ChemFOnt: Showing chemical card for UDP-D-Xylose (CFc000000805)

Record Information

Version

1.0

Creation Date

2022-08-28 10:25:12 UTC

Update Date

2022-09-13 18:45:18 UTC

Chemfont ID

CFc000000805

Molecule Identification

Common Name

UDP-D-Xylose

Definition

Uridine diphosphate xylose is important intermediate in the Nucleotide sugars metabolism and chondroitin sulfate biosynthesis (KEGG). The decarboxylation product of UDPglucuronic acid, which is used for formation of the xylosides of seryl hydroxyl groups in mucoprotein synthesis.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
UDP Xylose	ChEBI
UDP-D-Xylose	ChEBI
UDP-Xylose	ChEBI
UDPxylose	ChEBI
Uridine 5'-(trihydrogen diphosphate), p'-alpha-D-xylopyranosyl ester	ChEBI
Uridine diphosphate xylose	ChEBI
URIDINE-5'-diphosphATE-xylopyranose	ChEBI
Uridine 5'-(trihydrogen diphosphate), p'-a-D-xylopyranosyl ester	Generator
Uridine 5'-(trihydrogen diphosphate), p'-α-D-xylopyranosyl ester	Generator
Uridine 5'-(trihydrogen diphosphoric acid), p'-a-D-xylopyranosyl ester	Generator
Uridine 5'-(trihydrogen diphosphoric acid), p'-alpha-D-xylopyranosyl ester	Generator
Uridine 5'-(trihydrogen diphosphoric acid), p'-α-D-xylopyranosyl ester	Generator
Uridine diphosphoric acid xylose	Generator
URIDINE-5'-diphosphoric acid-xylopyranose	Generator
UDP-a-D-Xylose	Generator
UDP-Α-D-xylose	Generator
Diphosphate xylose, uridine	MeSH
Xylose, uridine diphosphate	MeSH
Xylose, UDP	MeSH
UDP alpha-D-xylose	HMDB
UDP α-D-xylose	HMDB
UDP-alpha-D-xylopyranose	HMDB
UDP-α-D-xylopyranose	HMDB
Uridine 5'-(trihydrogen diphosphate) mono-D-xylopyranosyl ester	HMDB
Uridine 5'-(trihydrogen pyrophosphate) mono-D-xylopyranosyl ester	HMDB
Uridine 5’-(trihydrogen diphosphate) mono-D-xylopyranosyl ester	HMDB
Uridine 5’-(trihydrogen pyrophosphate) mono-D-xylopyranosyl ester	HMDB
Uridine diphosphate D-xylose	HMDB
Uridine diphospho-alpha-D-xylopyranose	HMDB
Uridine diphospho-α-D-xylopyranose	HMDB
Uridine diphosphoxylose	HMDB

Chemical Formula

C₁₄H₂₂N₂O₁₆P₂

Average Molecular Weight

536.2758

Monoisotopic Molecular Weight

536.04445569

IUPAC Name

[({[(2R,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy})phosphinic acid

Traditional Name

udp-xylose

CAS Registry Number

3616-06-6

SMILES

O[C@@H]1[C@@H](COP(O)(=O)OP(O)(=O)O[C@H]2OC[C@@H](O)[C@H](O)[C@H]2O)O[C@H]([C@@H]1O)N1C=CC(=O)NC1=O

InChI Identifier

InChI=1S/C14H22N2O16P2/c17-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/t5-,6-,8+,9-,10-,11-,12-,13-/m1/s1

InChI Key

DQQDLYVHOTZLOR-OCIMBMBZSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside diphosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside diphosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Organic pyrophosphate
Monoalkyl phosphate
Pyrimidone
Hydroxypyrimidine
Hydropyrimidine
Monosaccharide
Alkyl phosphate
Organic phosphoric acid derivative
Pyrimidine
Oxane
Phosphoric acid ester
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Polyol
Organoheterocyclic compound
Azacycle
Oxacycle
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Alcohol
Organic oxygen compound
Organic nitrogen compound
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

UDP-sugar (CHEBI:16082 )

Functional Ontology

Not Available

Adipose tissue (HMDB: HMDB0001018)

Epithelium

Epidermis (HMDB: HMDB0001018)

Cell

Fibroblasts (HMDB: HMDB0001018)
Neuron (HMDB: HMDB0001018)

Organ

Cellular substructure

Organelle

Endoplasmic reticulum (HMDB: HMDB0001018)
Golgi apparatus (HMDB: HMDB0001018)

Source

Endogenous

Endogenous (HMDB: HMDB0001018)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Herb and spice mixture

Curry powder (FooDB: FOOD00678)

Vegetable

Cabbage

Onion-family vegetable

Root vegetable

Shoot vegetable

Leaf vegetable

Common beet (FooDB: FOOD00025)
Endive (FooDB: FOOD00048)
Rocket salad (ssp.) (FooDB: FOOD00077)
Swamp cabbage (FooDB: FOOD00091)
Lettuce (FooDB: FOOD00095)
Garden cress (FooDB: FOOD00099)
Spinach (FooDB: FOOD00178)
Swiss chard (FooDB: FOOD00237)
Chicory leaves (FooDB: FOOD00250)
Garland chrysanthemum (FooDB: FOOD00333)
Corn salad (FooDB: FOOD00340)
Jute (FooDB: FOOD00389)
Lambsquarters (FooDB: FOOD00394)
Malabar spinach (FooDB: FOOD00404)
New Zealand spinach (FooDB: FOOD00415)
Yautia (FooDB: FOOD00510)
Ostrich fern (FooDB: FOOD00556)
Romaine lettuce (FooDB: FOOD00888)
Iceberg lettuce (FooDB: FOOD00973)
Pea shoots (FooDB: FOOD00975)
Yau choy (FooDB: FOOD00976)
Water spinach (FooDB: FOOD00977)

Fruit vegetable

Pepper (FooDB: FOOD00040)
Olive (FooDB: FOOD00121)
Avocado (FooDB: FOOD00130)
Garden tomato (FooDB: FOOD00171)
Cherry tomato (FooDB: FOOD00172)
Garden tomato (var.) (FooDB: FOOD00173)
Eggplant (FooDB: FOOD00174)
Pepper (C. baccatum) (FooDB: FOOD00231)
Pepper (C. chinense) (FooDB: FOOD00232)
Pepper (Capsicum) (FooDB: FOOD00233)
Groundcherry (FooDB: FOOD00371)
Pepper (C. frutescens) (FooDB: FOOD00428)
Mexican groundcherry (FooDB: FOOD00491)
Pepper (C. pubescens) (FooDB: FOOD00849)
Green bell pepper (FooDB: FOOD00877)
Yellow bell pepper (FooDB: FOOD00878)
Orange bell pepper (FooDB: FOOD00879)
Red bell pepper (FooDB: FOOD00880)
Italian sweet red pepper (FooDB: FOOD00881)
Jalapeno pepper (FooDB: FOOD00955)
Cubanelle pepper (FooDB: FOOD00971)

Tuber

Stalk vegetable

Other vegetable

Giant butterbur (FooDB: FOOD00314)
Carob (FooDB: FOOD00321)
Chinese water chestnut (FooDB: FOOD00332)
Horseradish tree (FooDB: FOOD00379)
Sacred lotus (FooDB: FOOD00402)
Nopal (FooDB: FOOD00416)
Okra (FooDB: FOOD00420)
Sesbania flower (FooDB: FOOD00469)
Agave (FooDB: FOOD00563)
Narrowleaf cattail (FooDB: FOOD00564)
Heart of palm (FooDB: FOOD00718)
Tree fern (FooDB: FOOD00797)

Mushroom

Castanospermum australe (FooDB: FOOD00893)
Gentiana lutea (FooDB: FOOD00894)
Juniperus communis (FooDB: FOOD00895)
Albizia gummifera (FooDB: FOOD00896)

Fruit

Tropical fruit

Citrus

Lime (FooDB: FOOD00053)
Lemon (FooDB: FOOD00054)
Pummelo (FooDB: FOOD00055)
Mandarin orange (Clementine, Tangerine) (FooDB: FOOD00056)
Sweet orange (FooDB: FOOD00057)
Grapefruit/Pummelo hybrid (FooDB: FOOD00255)
Grapefruit (FooDB: FOOD00256)
Persian lime (FooDB: FOOD00543)
Sour orange (FooDB: FOOD00918)
Mikan (FooDB: FOOD00932)
Clementine (FooDB: FOOD00959)

Pome

Berry

Black crowberry (FooDB: FOOD00075)
Strawberry (FooDB: FOOD00083)
Black huckleberry (FooDB: FOOD00084)
Sea-buckthornberry (FooDB: FOOD00087)
Mulberry (FooDB: FOOD00116)
Black mulberry (FooDB: FOOD00117)
Black chokeberry (FooDB: FOOD00136)
Blackcurrant (FooDB: FOOD00155)
Redcurrant (FooDB: FOOD00156)
Gooseberry (FooDB: FOOD00157)
Cloudberry (FooDB: FOOD00161)
Red raspberry (FooDB: FOOD00162)
Black raspberry (FooDB: FOOD00163)
Black elderberry (FooDB: FOOD00166)
Rowanberry (FooDB: FOOD00176)
Vaccinium (Blueberry, Cranberry, Huckleberry) (FooDB: FOOD00188)
Lowbush blueberry (FooDB: FOOD00189)
Sparkleberry (FooDB: FOOD00190)
Highbush blueberry (FooDB: FOOD00191)
American cranberry (FooDB: FOOD00192)
Bilberry (FooDB: FOOD00193)
Lingonberry (FooDB: FOOD00194)
Muscadine grape (FooDB: FOOD00203)
Common grape (FooDB: FOOD00204)
Arctic blackberry (FooDB: FOOD00207)
Bayberry (FooDB: FOOD00209)
Elliott's blueberry (FooDB: FOOD00210)
Canada blueberry (FooDB: FOOD00211)
Bog bilberry (FooDB: FOOD00212)
Buffalo currant (FooDB: FOOD00213)
European cranberry (FooDB: FOOD00217)
Deerberry (FooDB: FOOD00218)
Cascade huckleberry (FooDB: FOOD00220)
Oval-leaf huckleberry (FooDB: FOOD00221)
Evergreen huckleberry (FooDB: FOOD00222)
Red huckleberry (FooDB: FOOD00223)
Summer grape (FooDB: FOOD00227)
Fox grape (FooDB: FOOD00228)
Half-highbush blueberry (FooDB: FOOD00248)
Jostaberry (FooDB: FOOD00257)
Sweet rowanberry (FooDB: FOOD00265)
Skunk currant (FooDB: FOOD00267)
Squashberry (FooDB: FOOD00344)
Elderberry (FooDB: FOOD00358)
Grape (FooDB: FOOD00369)
Alaska blueberry (FooDB: FOOD00380)
Loganberry (FooDB: FOOD00400)
Ohelo berry (FooDB: FOOD00419)
Salmonberry (FooDB: FOOD00456)
Strawberry guava (FooDB: FOOD00482)
Boysenberry (FooDB: FOOD00542)
Chinese bayberry (FooDB: FOOD00852)
Saskatoon berry (FooDB: FOOD00884)
Nanking cherry (FooDB: FOOD00885)
Rabbiteye blueberry (FooDB: FOOD00898)
Blackberry (FooDB: FOOD00906)
Partridge berry (FooDB: FOOD00931)
Green grape (FooDB: FOOD00964)
Red grape (FooDB: FOOD00965)
Black plum (FooDB: FOOD00966)
Black raisin (FooDB: FOOD00968)
Chinese plum (FooDB: FOOD00978)
Green plum (FooDB: FOOD00979)
Wampee (FooDB: FOOD00980)
Goji (FooDB: FOOD00982)
Monk fruit (FooDB: FOOD00983)
Hawthorn (FooDB: FOOD00985)
Lantern fruit (FooDB: FOOD00986)
Cape gooseberry (FooDB: FOOD00988)

Other fruit

Fig (FooDB: FOOD00081)
Date (FooDB: FOOD00135)
Jujube (FooDB: FOOD00388)

Drupe

Prunus (Cherry, Plum) (FooDB: FOOD00143)
Apricot (FooDB: FOOD00144)
Sweet cherry (FooDB: FOOD00145)
Sour cherry (FooDB: FOOD00146)
European plum (FooDB: FOOD00147)
Peach (FooDB: FOOD00149)
Nectarine (FooDB: FOOD00229)
Peach (var.) (FooDB: FOOD00230)
Common chokecherry (FooDB: FOOD00562)

Nut

Cashew nut (FooDB: FOOD00011)
Peanut (FooDB: FOOD00016)
Brazil nut (FooDB: FOOD00024)
Pecan nut (FooDB: FOOD00044)
Chestnut (FooDB: FOOD00045)
Common hazelnut (FooDB: FOOD00062)
Black walnut (FooDB: FOOD00093)
Common walnut (FooDB: FOOD00094)
Pine nut (FooDB: FOOD00138)
Pistachio (FooDB: FOOD00140)
Almond (FooDB: FOOD00148)
Macadamia nut (M. tetraphylla) (FooDB: FOOD00225)
Japanese walnut (FooDB: FOOD00240)
Acorn (FooDB: FOOD00282)
Beech nut (FooDB: FOOD00299)
Butternut (FooDB: FOOD00316)
Chinese chestnut (FooDB: FOOD00331)
European chestnut (FooDB: FOOD00363)
Hazelnut (FooDB: FOOD00376)
Hickory nut (FooDB: FOOD00377)
Japanese chestnut (FooDB: FOOD00385)
Pili nut (FooDB: FOOD00432)
Colorado pinyon (FooDB: FOOD00433)
Macadamia nut (FooDB: FOOD00525)
Walnut (FooDB: FOOD00608)

Cereal and cereal product

Cereal

Cereal product

Pasta (FooDB: FOOD00273)
Bulgur (FooDB: FOOD00741)
Semolina (FooDB: FOOD00745)
Flour (FooDB: FOOD00799)

Dough

Sourdough (FooDB: FOOD00275)

Leavened bread

Flat bread

Other bread

Potato bread (FooDB: FOOD00811)

Sweet bread

Raisin bread (FooDB: FOOD00817)

Pulse

Pea

Lentil

Lentils (FooDB: FOOD00098)

Other pulse

Lupine (FooDB: FOOD00104)
White lupine (FooDB: FOOD00403)

Bean

Green lentil (FooDB: FOOD00970)

Gourd

Watermelon (FooDB: FOOD00052)
Muskmelon (FooDB: FOOD00064)
Cucumber (FooDB: FOOD00065)
Cucurbita (FooDB: FOOD00066)
Bitter gourd (FooDB: FOOD00115)
Winter squash (FooDB: FOOD00283)
Butternut squash (FooDB: FOOD00317)
Calabash (FooDB: FOOD00318)
Chayote (FooDB: FOOD00325)
Towel gourd (FooDB: FOOD00492)
Wax gourd (FooDB: FOOD00499)
Tinda (FooDB: FOOD00559)
Horned melon (FooDB: FOOD00761)
Sunburst squash (pattypan squash) (FooDB: FOOD00874)
Green zucchini (FooDB: FOOD00875)
Yellow zucchini (FooDB: FOOD00876)
Japanese pumpkin (FooDB: FOOD00886)
Acorn squash (FooDB: FOOD00972)
Cantaloupe melon (FooDB: FOOD00984)

Coffee and coffee product

Coffee

Arabica coffee (FooDB: FOOD00059)
Robusta coffee (FooDB: FOOD00060)

Soy

Soy bean (FooDB: FOOD00085)

Soy product

Soy sauce (FooDB: FOOD00694)
Miso (FooDB: FOOD00695)
Tofu (FooDB: FOOD00696)
Soy milk (FooDB: FOOD00736)
Soy cream (FooDB: FOOD00784)

Dish

Other dish

Taco shell (FooDB: FOOD00991)
Tostada shell (FooDB: FOOD00992)

Tea

Herbal tea

Hibiscus tea (FooDB: FOOD00723)
Greenthread tea (FooDB: FOOD00820)

Baking good

Wrapper

Wonton wrapper (FooDB: FOOD00818)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Nucleotide Sugars Metabolism (PathBank: SMP0087302)
Anthocyanidin Sambubioside Biosynthesis (PathBank: SMP0012030)

Disease pathway

Galactosemia III (PathBank: SMP0120561)
Galactosemia II (GALK) (PathBank: SMP0120560)

Role

Not Available

Physical Properties

Predicted Properties

Property	Value	Source
Water Solubility	13.6 g/L	ALOGPS
logP	-1.3	ALOGPS
logP	-4.4	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	271.31 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	100.49 m³·mol⁻¹	ChemAxon
Polarizability	42.57 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

HMDB0001018

DrugBank ID

DB01713

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB005661

KNApSAcK ID

Not Available

Chemspider ID

18152

KEGG Compound ID

C00190

BioCyc ID

UDP-D-XYLOSE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5948

PubChem Compound

19235

PDB ID

Not Available

ChEBI ID

16082

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Ernst, Christiane; Klaffke, Werner. Chemical Synthesis of Uridine Diphospho-D-xylose and UDP-L-arabinose. Journal of Organic Chemistry (2003), 68(14), 5780-5783.

Showing chemical card for UDP-D-Xylose (CFc000000805)

MOL for CFc000000805 (UDP-D-Xylose)

3D MOL for CFc000000805 (UDP-D-Xylose)

3D SDF for CFc000000805 (UDP-D-Xylose)

3D-SDF for CFc000000805 (UDP-D-Xylose)

PDB for CFc000000805 (UDP-D-Xylose)

3D PDB for CFc000000805 (UDP-D-Xylose)

SMILES for CFc000000805 (UDP-D-Xylose)

INCHI for CFc000000805 (UDP-D-Xylose)

Structure for CFc000000805 (UDP-D-Xylose)

3D Structure for CFc000000805 (UDP-D-Xylose)