ChemFOnt: Showing chemical card for 3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid (CFc000136279)

Record Information

Version

1.0

Creation Date

2022-08-28 10:25:12 UTC

Update Date

2022-09-13 22:09:43 UTC

Chemfont ID

CFc000136279

Molecule Identification

Common Name

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

Definition

Orotidine, also known as 6-carboxyuridine, 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. In humans, orotidine is involved in the metabolic disorder called the dimethylglycine dehydrogenase deficiency pathway. Orotidine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Orotidine, with regard to humans, has been found to be associated with the diseases such as uremia; orotidine has also been linked to the inborn metabolic disorder orotic aciduria I. Based on a literature review a significant number of articles have been published on Orotidine.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
3-Ribofuranosylorotic acid	ChEBI
6-Carboxyuridine	ChEBI
3-Ribofuranosylorotate	Generator
Orotic acid riboside	HMDB
Orotidine, ammonium salt	HMDB

Chemical Formula

C₁₀H₁₂N₂O₈

Average Molecular Weight

288.2109

Monoisotopic Molecular Weight

288.05936537

IUPAC Name

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

Traditional Name

orotidine

CAS Registry Number

314-50-1

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C(=O)NC(=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)/t4-,6-,7-,8-/m1/s1

InChI Key

FKCRAVPPBFWEJD-XVFCMESISA-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
Hydroxypyrimidine
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Azacycle
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Carboxylic acid
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organonitrogen compound
Alcohol
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organic oxide
Primary alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

uridines (CHEBI:25722 )
pyrimidinemonocarboxylic acid (CHEBI:25722 )
nucleoside (CHEBI:25722 )

Functional Ontology

Not Available

Not Available

Not Available

Not Available

Physical Properties

Predicted Properties

Property	Value	Source
Water Solubility	44.7 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.8	ChemAxon
logS	-0.81	ALOGPS
pKa (Strongest Acidic)	2.86	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	156.63 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	59.87 m³·mol⁻¹	ChemAxon
Polarizability	25 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

HMDB0000788

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Orotidine

METLIN ID

5754

PubChem Compound

92751

PDB ID

Not Available

ChEBI ID

25722

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

Showing chemical card for 3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid (CFc000136279)

MOL for CFc000136279 (3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid)

3D MOL for CFc000136279 (3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid)

3D SDF for CFc000136279 (3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid)

3D-SDF for CFc000136279 (3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid)

PDB for CFc000136279 (3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid)

3D PDB for CFc000136279 (3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid)

SMILES for CFc000136279 (3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid)

INCHI for CFc000136279 (3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid)

Structure for CFc000136279 (3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid)

3D Structure for CFc000136279 (3-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid)