P. aeruginosa Metabolome Database: UDP (PAMDB110529)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB110529

Identification

Name:

UDP

Description:

An organophosphate oxoanion arising from deprotonation of the diphosphate OH groups of uridine 5'-diphosphate; major species at pH 7.3.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

uridine-diphosphate
uridine-5'-diphosphate

Chemical Formula:

C₉H₁₁N₂O₁₂P₂

Average Molecular Weight:

401.14

Monoisotopic Molecular Weight:

404.002196945

InChI Key:

XCCTYIAWTASOJW-XVFCMESISA-K

InChI:

InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/p-3/t4-,6-,7-,8-/m1/s1

CAS number:

58-98-0

IUPAC Name:

5'-O-[(phosphonatooxy)phosphinato]uridine

Traditional IUPAC Name:

UDP

SMILES:

C(OP(=O)([O-])OP(=O)([O-])[O-])C1(OC(C(O)C(O)1)N2(C=CC(=O)NC(=O)2))

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of chemical entities known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Chemical entities

Super Class

Organic compounds

Class

Nucleosides, nucleotides, and analogues

Sub Class

Pyrimidine nucleotides

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
Hydroxypyrimidine
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Oxolane
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Alcohol
Organopnictogen compound
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine ribonucleoside 5'-diphosphate (CHEBI:17659 )
uridine 5'-phosphate (CHEBI:17659 )
Ribonucleotides (C00015 )

Physical Properties

State:

Solid

Charge:

-3

Melting point:

Not Available

Experimental Properties:

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	8.89 mg/mL	ALOGPS
logP	-0.94	ALOGPS
logP	-3	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	212.39 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	74.31 m³·mol^-1	ChemAxon
Polarizability	30.41 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Not Available

Reactions:

UDP-α-D-glucose + β-D-fructofuranose 6-phosphate → sucrose 6F-phosphate + UDP + Hydrogen ion
Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose + di-trans,octa-cis-undecaprenyl phosphate → 4-deoxy-4-formamido-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate + UDP
UDP-N-acetyl-α-D-glucosamine + Water → N-acetyl-α-D-mannosamine + UDP + Hydrogen ion
decaprenyl-diphospho-N-acetylmuramoyl-pentapeptide + UDP-N-acetyl-α-D-glucosamine → Hydrogen ion + decaprenyl-pyrophosphoryl-(N-acetylglucosamine)-N-acetylmuramyl-(pentapeptide) + UDP
undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-L-lysyl- D-alanine + UDP-N-acetyl-α-D-glucosamine → Hydrogen ion + undecaprenyl-diphospho-(N-acetylglucosamine)-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-L-lysyl-D-alanine + UDP
undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-L-lysyl- D-alanyl-D-alanine + UDP-N-acetyl-α-D-glucosamine → Hydrogen ion + undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl-L-alanyl-γ-D-glutamyl-L-lysyl-D-alanyl-D-alanine + UDP
UDP-α-D-glucose + D-Fructose → Sucrose + UDP + Hydrogen ion
UDP-α-D-glucose + galactosyl-(glucosyl)2-(heptosyl)3-Kdo2-lipid A-bisphosphate → Hydrogen ion + galactosyl-(glucosyl)3-(heptosyl)3-Kdo2-lipid A-bisphosphate + UDP
UDP-α-D-glucose + galactosyl-glucosyl-(heptosyl)3-Kdo2-lipid A-bisphosphate → Hydrogen ion + galactosyl-(glucosyl)2-(heptosyl)3-Kdo2-lipid A-bisphosphate + UDP
UDP-α-D-glucose + Glucopyranose → Trehalose + UDP + Hydrogen ion
UDP-α-D-galactose + glucosyl-(heptosyl)3-Kdo2-lipid A-bisphosphate → Hydrogen ion + galactosyl-glucosyl-(heptosyl)3-Kdo2-lipid A-bisphosphate + UDP
UDP-α-D-glucose + (heptosyl)2-Kdo2-lipid A → Hydrogen ion + glucosyl-(heptosyl)2-Kdo2-lipid A + UDP

Pathways:

Amino Sugar Metabolism pae00520
Androgen and Estrogen Metabolism pae00150
Galactose Metabolism pae00052
Porphyrin Metabolism pae00860
Pyrimidine Metabolism pae00240
Sphingolipid Metabolism pae00500
Starch and Sucrose Metabolism pae00500

Spectra

Spectra:

Spectrum Type	Description	Splash Key
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0002-9000000000-7c065a8df0e08b8c365f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0002-9000000000-73234233232c376d095c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0002-9000000000-7c065a8df0e08b8c365f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-0pdi-6910600000-bf4136774851b6559f17	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available
1D NMR	1H NMR Spectrum	Not Available
1D NMR	1H NMR Spectrum	Not Available
1D NMR	13C NMR Spectrum	Not Available
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available

References

References:

Kim HY, Thomas D, Hanley MR (1996)Stimulation of Ca(2+)-dependent membrane currents in Xenopus oocytes by microinjection of pyrimidine nucleotide-glucose conjugates. Molecular pharmacology 49, Pubmed: 8632770

Synthesis Reference:

Zeng, Bin; Rao, Linfan; Li, Gaowo. Method for manufacturing uridine diphosphate. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 14pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

Links

External Links:

Resource	Link
CAS	58-98-0
ChEBI	58223
ChemSpider	16739715
HMDB	HMDB00295
IAF1260	33518
KEGG	C00015
KNApSAcK	C00007313
MetaboLights	MTBLC58223
PubChem	20056717

UDP (PAMDB110529)

Structure for UDP (PAMDB110529)