Bovine Metabolome Database: Showing metabocard for Uridine 5'-diphosphate (BMDB0000295)

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Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (12) Show 12 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:27:59 UTC

Update Date

2020-05-21 16:29:27 UTC

BMDB ID

BMDB0000295

Secondary Accession Numbers

BMDB00295

Metabolite Identification

Common Name

Uridine 5'-diphosphate

Description

Uridine 5'-diphosphate, also known as 5'-UDP or uridine diphosphoric acid, belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. Uridine 5'-diphosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Uridine 5'-diphosphate exists in all living species, ranging from bacteria to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
Uridine diphosphate	ChEBI
Uridine diphosphoric acid	Generator
Uridine 5'-diphosphoric acid	Generator
5'-UDP	HMDB
UDP	HMDB
Uridine 5'-pyrophosphate	HMDB
Uridine 5'-pyrophosphorate	HMDB
Uridine 5'-pyrophosphoric acid	HMDB
Uridine pyrophosphate	HMDB
Pyrophosphate, uridine	HMDB
Diphosphate, uridine	HMDB
5’-UDP	HMDB
Uridine 5'-(trihydrogen pyrophosphate)	HMDB
Uridine 5'-diphosphate	HMDB
Uridine 5’-(trihydrogen pyrophosphate)	HMDB
Uridine 5’-diphosphate	HMDB
Uridine 5’-diphosphoric acid	HMDB
Uridine 5’-pyrophosphate	HMDB
Uridine 5’-pyrophosphoric acid	HMDB

Chemical Formula

C₉H₁₄N₂O₁₂P₂

Average Molecular Weight

404.1612

Monoisotopic Molecular Weight

404.002196946

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]phosphonic acid

Traditional Name

UDP

CAS Registry Number

58-98-0

SMILES

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

InChI Identifier

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)/t4-,6-,7-,8-/m1/s1

InChI Key

XCCTYIAWTASOJW-XVFCMESISA-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
Hydroxypyrimidine
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Tetrahydrofuran
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 )

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cytoplasm
Endoplasmic reticulum
Golgi
Lysosome
Mitochondria
Nucleus

Physical Properties

State

Solid

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
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	30.43 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-4911000000-e0e7874495a5b5baf6b1	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00pi-3795210000-ef08b4deabe40209df75	View in MoNA
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
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0pdi-6910600000-bf4136774851b6559f17	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1901000000-4c9ba16543da8ee18c74	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4901000000-1ff9973ec00da457d453	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-7900000000-f88f01d934d46a57fefb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0ik9-3904300000-454bc02fb8862a1d0fac	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-057l-9801000000-5aabcad933dc7e5003a8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-7a6d480c699f409f2f36	View in MoNA
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cytoplasm
Endoplasmic reticulum
Golgi
Lysosome
Mitochondria
Nucleus

Biospecimen Locations

Placenta
Prostate Tissue
Thyroid Gland

Pathways

Name	SMPDB/Pathwhiz	KEGG
Amino Sugar Metabolism		Not Available
Galactose Metabolism		Not Available
Lactose Synthesis		Not Available
Porphyrin Metabolism		Not Available
Pyrimidine Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Prostate Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Thyroid Gland	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000295

DrugBank ID

DB03435

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

Not Available

PubChem Compound

6031

PDB ID

Not Available

ChEBI ID

17659

References

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)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Nucleoside diphosphate kinase 7

General function:: Nucleotide transport and metabolism
Specific function:: Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity).
Gene Name:: NME7
Uniprot ID:: Q5E9Y9
Molecular weight:: 42599.0

Reactions

Uridine triphosphate + ADP → Uridine 5'-diphosphate + Adenosine triphosphate	details

Enzyme Details

2. Nucleoside diphosphate kinase B

General function:: Nucleotide transport and metabolism
Specific function:: Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity). Negatively regulates Rho activity by interacting with AKAP13/LBC. Acts as a transcriptional activator of the MYC gene; binds DNA non-specifically. Binds to both single-stranded guanine- and cytosine-rich strands within the nuclease hypersensitive element (NHE) III(1) region of the MYC gene promoter. Does not bind to duplex NHE III(1). Has G-quadruplex (G4) DNA-binding activity, which is independent of its nucleotide-binding and kinase activity. Binds both folded and unfolded G4 with similar low nanomolar affinities. Stabilizes folded G4s regardless of whether they are prefolded or not (By similarity). Exhibits histidine protein kinase activity (PubMed:12486123).
Gene Name:: NME2
Uniprot ID:: Q3T0Q4
Molecular weight:: 17316.0

Reactions

Adenosine triphosphate + Uridine 5'-diphosphate → ADP + Uridine triphosphate	details

Enzyme Details

3. GTP:AMP phosphotransferase AK3, mitochondrial

General function:: Nucleotide transport and metabolism
Specific function:: Involved in maintaining the homeostasis of cellular nucleotides by catalyzing the interconversion of nucleoside phosphates. Has GTP:AMP phosphotransferase and ITP:AMP phosphotransferase activities.
Gene Name:: AK3
Uniprot ID:: P08760
Molecular weight:: 25671.0

Reactions

Uridine 5'-diphosphate + ADP → Uridine triphosphate + 3'-AMP	details

Enzyme Details

4. Beta-1,4-galactosyltransferase 1

General function:: Involved in alpha-tubulin binding
Specific function:: The Golgi complex form catalyzes the production of lactose in the lactating mammary gland and could also be responsible for the synthesis of complex-type N-linked oligosaccharides in many glycoproteins as well as the carbohydrate moieties of glycolipids.
Gene Name:: B4GALT1
Uniprot ID:: P08037
Molecular weight:: 44843.0

Reactions

Uridine diphosphategalactose + D-Glucose → Uridine 5'-diphosphate + Alpha-Lactose	details
D-Glucose + Uridine diphosphategalactose → Uridine 5'-diphosphate + Alpha-Lactose	details

Enzyme Details

5. UDP-glucuronosyltransferase 3A1

General function:: Carbohydrate transport and metabolism
Specific function:: UDP-glucuronosyltransferases catalyze phase II biotransformation reactions in which lipophilic substrates are conjugated with glucuronic acid to increase water solubility and enhance excretion. They are of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds (By similarity).
Gene Name:: UGT3A1
Uniprot ID:: Q1LZI1
Molecular weight:: 59682.0

Reactions

Uridine diphosphate glucuronic acid → Isovalerylglucuronide + Uridine 5'-diphosphate	details

Enzyme Details

6. Glycogen [starch] synthase, muscle

General function:: Cell wall/membrane/envelope biogenesis
Specific function:: Transfers the glycosyl residue from UDP-Glc to the non-reducing end of alpha-1,4-glucan.
Gene Name:: GYS1
Uniprot ID:: A7MB78
Molecular weight:: 83814.0

Reactions

Uridine diphosphate glucose → Amylose + Uridine 5'-diphosphate	details

Enzyme Details

7. UMP-CMP kinase

General function:: Nucleotide transport and metabolism
Specific function:: Catalyzes the phosphorylation of pyrimidine nucleoside monophosphates at the expense of ATP. Plays an important role in de novo pyrimidine nucleotide biosynthesis. Has preference for UMP and CMP as phosphate acceptors. Also displays broad nucleoside diphosphate kinase activity.
Gene Name:: CMPK1
Uniprot ID:: Q2KIW9
Molecular weight:: 22279.0

Reactions

Adenosine triphosphate + Uridine 5'-monophosphate → ADP + Uridine 5'-diphosphate	details

Enzyme Details

8. Alpha-lactalbumin

General function:: Involved in calcium ion binding
Specific function:: Regulatory subunit of lactose synthase, changes the substrate specificity of galactosyltransferase in the mammary gland making glucose a good acceptor substrate for this enzyme. This enables LS to synthesize lactose, the major carbohydrate component of milk. In other tissues, galactosyltransferase transfers galactose onto the N-acetylglucosamine of the oligosaccharide chains in glycoproteins.
Gene Name:: LALBA
Uniprot ID:: P00711
Molecular weight:: 16247.0

Reactions

D-Glucose + Uridine diphosphategalactose → Uridine 5'-diphosphate + Alpha-Lactose	details

Enzyme Details

9. Glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase

General function:: Not Available
Specific function:: Not Available
Gene Name:: GNE
Uniprot ID:: F1MIL9
Molecular weight:: 79390.0

Reactions

Uridine diphosphate-N-acetylglucosamine + Water → N-Acetyl-D-mannosamine + Uridine 5'-diphosphate	details

Enzyme Details

10. Calcium activated nucleotidase 1

General function:: Not Available
Specific function:: Not Available
Gene Name:: CANT1
Uniprot ID:: E1BGL5
Molecular weight:: 44706.0

Reactions

Uridine 5'-diphosphate + Water → Uridine 5'-monophosphate + Hydrogen phosphate	details
Uridine triphosphate + Water → Uridine 5'-diphosphate + Hydrogen phosphate	details

Enzyme Details

11. Cytidine/uridine monophosphate kinase 2

General function:: Not Available
Specific function:: Not Available
Gene Name:: CMPK2
Uniprot ID:: F1N2W6
Molecular weight:: 64396.0

Reactions

Uridine 5'-monophosphate + Adenosine triphosphate → Uridine 5'-diphosphate + ADP	details

Enzyme Details

12. Ribonucleotide reductase regulatory subunit M2

General function:: Not Available
Specific function:: Not Available
Gene Name:: RRM2
Uniprot ID:: E1BI58
Molecular weight:: 44821.0

Reactions

Uridine 5'-diphosphate + Thioredoxin disulfide + Water → dUDP + Thioredoxin	details

Showing metabocard for Uridine 5'-diphosphate (BMDB0000295)

Structure for BMDB0000295 (Uridine 5'-diphosphate)

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