ECMDB: Orotidylic acid (ECMDB00218) (M2MDB000090)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (2)XML

Proteins (862)

Record Information

Version

2.0

Creation Date

2012-05-31 10:23:59 -0600

Update Date

2015-06-03 15:53:24 -0600

Secondary Accession Numbers

ECMDB00218

Identification

Name:

Orotidylic acid

Description

Orotidylic acid (OMP), is a pyrimidine nucleotide which is the last intermediate in the biosynthesis of uridine monophosphate. Decarboxylation by Orotidylate decarboxylase affords Uridine 5'-phosphate which is the route to Uridine and its derivatives de novo and consequently one of the most important processes in nucleic acid synthesis (Dictionary of Organic Compounds). In E. coli, the enzyme UMP synthase converts OMP into uridine 5'- monophosphate. If UMP synthase is defective, orotic aciduria can result. (Wikipedia)

Structure

MOL SDF PDB SMILES InChI

Synonyms:

1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-D-ribofuranosyl)-4-Pyrimidinecarboxylate
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-D-ribofuranosyl)-4-Pyrimidinecarboxylic acid
1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-delta-Ribofuranosyl)-4-pyrimidinecarboxylate
1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-delta-Ribofuranosyl)-4-pyrimidinecarboxylic acid
1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-δ-Ribofuranosyl)-4-pyrimidinecarboxylate
1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-δ-Ribofuranosyl)-4-pyrimidinecarboxylic acid
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-Pyrimidinecarboxylate
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-Pyrimidinecarboxylic acid
1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-β-δ-Ribofuranosyl)-4-pyrimidinecarboxylate
1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-β-δ-Ribofuranosyl)-4-pyrimidinecarboxylic acid
2,6-dioxo-3-(5-O-phosphono-b-D-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
2,6-dioxo-3-(5-O-phosphono-b-D-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
2,6-dioxo-3-(5-O-phosphono-b-delta-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
2,6-dioxo-3-(5-O-phosphono-b-delta-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
2,6-dioxo-3-(5-O-phosphono-b-δ-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
2,6-dioxo-3-(5-O-phosphono-b-δ-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
2,6-Dioxo-3-(5-O-phosphono-beta-D-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
2,6-Dioxo-3-(5-O-phosphono-beta-D-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
2,6-Dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
2,6-Dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
2,6-dioxo-3-(5-O-phosphono-β-D-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
2,6-dioxo-3-(5-O-phosphono-β-D-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
2,6-dioxo-3-(5-O-phosphono-β-δ-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
2,6-dioxo-3-(5-O-phosphono-β-δ-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
5'-(Dihydrogen phosphate) 6-carboxy-uridine
5'-(Dihydrogen phosphate) Orotidine
5'-(Dihydrogen phosphoric acid) 6-carboxy-uridine
5'-(Dihydrogen phosphoric acid) orotidine
5'-OMP
5'-Phosphate Orotidine
5'-Phosphoric acid orotidine
5-(Dihydrogen phosphate)orotidine
5-(Dihydrogen phosphoric acid)orotidine
6-Carboxy-5'-uridylate
6-Carboxy-5'-uridylic acid
Ometoprim
OMP
Omp (nucleotide)
Orotidine 5'-(dihydrogen phosphate)
Orotidine 5'-(dihydrogen phosphoric acid)
Orotidine 5'-monophosphate
Orotidine 5'-monophosphoric acid
Orotidine 5'-phosphate
Orotidine 5'-phosphoric acid
Orotidine monophosphate
Orotidine monophosphoric acid
Orotidine-5'-phosphate
Orotidine-5'-phosphoric acid
Orotidine5'P
Orotidylate
Orotidylic acid

Chemical Formula:

C₁₀H₁₃N₂O₁₁P

Weight:

Average: 368.1908
Monoisotopic: 368.02569578

InChI Key:

KYOBSHFOBAOFBF-XVFCMESISA-N

InChI:

InChI=1S/C10H13N2O11P/c13-5-1-3(9(16)17)12(10(18)11-5)8-7(15)6(14)4(23-8)2-22-24(19,20)21/h1,4,6-8,14-15H,2H2,(H,16,17)(H,11,13,18)(H2,19,20,21)/t4-,6-,7-,8-/m1/s1

CAS number:

2149-82-8

IUPAC Name:

3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid

Traditional IUPAC Name:

6-carboxy-5'-uridylic acid

SMILES:

O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(O)=O)N1C(=O)NC(=O)C=C1C(O)=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate 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 monophosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside monophosphate
Pentose-5-phosphate
Pentose phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Pentose monosaccharide
Pyrimidine-6-carboxylic acid or derivatives
Pyrimidine-6-carboxylic acid
Hydropyrimidine carboxylic acid derivative
Monoalkyl phosphate
Pyrimidone
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Pyrimidine
Alkyl phosphate
Phosphoric acid ester
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Secondary alcohol
Urea
Lactam
1,2-diol
Organoheterocyclic compound
Carboxylic acid derivative
Carboxylic acid
Azacycle
Monocarboxylic acid or derivatives
Oxacycle
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organooxygen compound
Organic nitrogen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine ribonucleoside 5'-monophosphate (CHEBI:15842 )

Physical Properties

State:

Solid

Charge:

-3

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	8.61 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-2.9	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.21	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	203.16 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	70.74 m³·mol⁻¹	ChemAxon
Polarizability	29.65 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:

Cytoplasm

Reactions:

Hydrogen ion + Orotidylic acid <> Carbon dioxide + Uridine 5'-monophosphate
Orotidylic acid + Pyrophosphate <> Orotic acid + Phosphoribosyl pyrophosphate
Orotidylic acid <> Uridine 5'-monophosphate + Carbon dioxide
Hydrogen ion + Orotidylic acid > Carbon dioxide + Uridine 5'-monophosphate
Orotidylic acid + Pyrophosphate > Orotic acid + Phosphoribosyl pyrophosphate
Orotidylic acid > Uridine 5'-monophosphate + Carbon dioxide
Orotic acid + Phosphoribosyl pyrophosphate > Pyrophosphate + Orotidylic acid
Hydrogen ion + Orotidylic acid <> Carbon dioxide + Uridine 5'-monophosphate
Orotidylic acid + Pyrophosphate <> Orotic acid + Phosphoribosyl pyrophosphate
Orotidylic acid + Pyrophosphate <> Orotic acid + Phosphoribosyl pyrophosphate

SMPDB Pathways:

Pyrimidine metabolism

PW000942

KEGG Pathways:

Drug metabolism - other enzymes ec00983
Metabolic pathways eco01100
Pyrimidine metabolism ec00240

EcoCyc Pathways:

uridine-5'-phosphate biosynthesis PWY-5686

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9512000000-a3f8062edabfeda1eaa8	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0002-9221230000-0c722324f49458fdfb65	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0914000000-3337770bad1b3ba8486c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4i-1911000000-f94acf2aa5da3364c517	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-5900000000-81a1aba75871162fc05b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0axv-8917000000-d1de3bc4514e88dd288c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056r-9701000000-13540f203bff602cb8f5	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-2bf7c464e9b79ae5c6a9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-2009000000-9ea216a0949682e0fe1f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9101000000-fef21032aec9be94593f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-8b5f1e6eeb57e5800b69	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01b9-0977000000-d51bb310da0232d1c1bb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0cdi-0930000000-504b86c3d067b5715b14	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-05mk-4900000000-c8b6c09c13fc530cdcc4	View in MoNA
1D NMR	13C 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
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C 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
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C 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
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C 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
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C 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
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411
Traut TW: Uridine-5'-phosphate synthase: evidence for substrate cycling involving this bifunctional protein. Arch Biochem Biophys. 1989 Jan;268(1):108-15. Pubmed: 2912371
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064

Synthesis Reference:

Ueda, Tohru; Yamamoto, Miyako; Yamane, Akira; Imazawa, Masaoki; Inoue, Hideo. Nucleosides and nucleotides. XXIII. Conversion of uridine nucleotides to the 6-cyano derivatives: synthesis of orotidylic acid. Journal of Carbohydrates, Nucleosides, Nuc

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	15842
HMDB ID	HMDB00218
Pubchem Compound ID	160617
Kegg ID	C01103
ChemSpider ID	141140
Wikipedia	Orotidylic acid
BioCyc ID	OROTIDINE-5-PHOSPHATE
EcoCyc ID	OROTIDINE-5-PHOSPHATE
Ligand Expo	OMP

Enzymes

Protein Details

1. Orotidine 5'-phosphate decarboxylase

General function:: Involved in catalytic activity
Specific function:: Catalyzes the decarboxylation of orotidine 5'- monophosphate (OMP) to uridine 5'-monophosphate (UMP)
Gene Name:: pyrF
Uniprot ID:: P08244
Molecular weight:: 26350

Reactions

Orotidine 5'-phosphate = UMP + CO(2).

Protein Details

2. Orotate phosphoribosyltransferase

General function:: Involved in orotate phosphoribosyltransferase activity
Specific function:: Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)
Gene Name:: pyrE
Uniprot ID:: P0A7E3
Molecular weight:: 23567

Reactions

Orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate.

Orotidylic acid (ECMDB00218) (M2MDB000090)

Structure for #<Compound:0xa6a0cf5c>

Enzymes

Reactions

Reactions