ChemFOnt: Showing chemical card for Orotidine (CFc000000628)

Record Information

Version

1.0

Creation Date

2022-08-28 10:25:12 UTC

Update Date

2022-09-13 18:45:04 UTC

Chemfont ID

CFc000000628

Molecule Identification

Common Name

Orotidine

Definition

Orotidine is a nucleoside formed by attaching orotic acid to a ribose ring via a beta-N1-glycosidic bond. It is a water-soluble solid. Orotidine is found in bacteria, fungi, plants, and animals. In humans, orotidine occurs as its 5'-phosphate (orotidylic acid), which is an intermediate in the biosynthesis of pyrimidine nucleosides (cytidine and uridine) that are found in nucleic acids (as the nucleotides containing the bases cytosine and uracil). Orotidine itself is not a component of nucleic acid. Orotidine monophosphate (OMP) is converted to uridine monophosphate by OMP decarboxylase, which is inhibited by mononucleotide precursors. Large amounts of orotidine are excreted in the urine of cancer patients treated with 6-azauridine, which is one such inhibitor, indicating that the subject has increased DNA synthesis due to cancer. Orotidine was first isolated from a mutant strain of the fungus Neurospora by A. Michael Michelson, William Drell, and Herschel K. Mitchell (PMID: 14853953 ).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Not Available

Chemical Formula

C₁₀H₁₂N₂O₈

Average Molecular Weight

288.2109

Monoisotopic Molecular Weight

288.05936537

IUPAC Name

3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid

Traditional Name

3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxopyrimidine-4-carboxylic acid

CAS Registry Number

314-50-1

SMILES

OCC1OC(C(O)C1O)N1C(=O)N=C(O)C=C1C(O)=O

InChI Identifier

InChI=1S/C10H12N2O8/c13-2-4-6(15)7(16)8(20-4)12-3(9(17)18)1-5(14)11-10(12)19/h1,4,6-8,13,15-16H,2H2,(H,17,18)(H,11,14,19)

InChI Key

FKCRAVPPBFWEJD-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Hydropyrimidine carboxylic acid derivative
Pyrimidine-6-carboxylic acid
Pyrimidine-6-carboxylic acid or derivatives
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Lactam
Urea
Secondary alcohol
Azacycle
Oxacycle
Monocarboxylic acid or derivatives
Carboxylic acid
Organoheterocyclic compound
Carboxylic acid derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Alcohol
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 7877593)

Organ

Placenta (HMDB: HMDB0000788)

Excreta

Biofluid or Excreta

Urine (PMID: 25757096)

Cellular substructure

Cytoplasm (HMDB: HMDB0000788)

Source

Endogenous

Endogenous (HMDB: HMDB0000788)

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)

Pulse

Bean

Yellow wax bean (FooDB: FOOD00882)
Green bean (FooDB: FOOD00883)

Pulses (FooDB: FOOD00867)

Process

Not Available

Role

Industrial application

Pharmaceutical industry

Biomarker

Orotic Aciduria (MarkerDB: MDB00000252)

Physical Properties

Predicted Properties

Property	Value	Source
Water Solubility	33.5 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-2.4	ChemAxon
logS	-0.93	ALOGPS
pKa (Strongest Acidic)	3.43	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	160.12 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	60.19 m³·mol⁻¹	ChemAxon
Polarizability	24.89 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB012085

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Orotidine

METLIN ID

Not Available

PubChem Compound

12313774

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Curra, William V.; Angle, Robert B. Synthesis of orotidine. Tetrahedron Letters (1963), (8), 533-5.

Showing chemical card for Orotidine (CFc000000628)

MOL for CFc000000628 (Orotidine)

3D MOL for CFc000000628 (Orotidine)

3D SDF for CFc000000628 (Orotidine)

3D-SDF for CFc000000628 (Orotidine)

PDB for CFc000000628 (Orotidine)

3D PDB for CFc000000628 (Orotidine)

SMILES for CFc000000628 (Orotidine)

INCHI for CFc000000628 (Orotidine)

Structure for CFc000000628 (Orotidine)

3D Structure for CFc000000628 (Orotidine)