NP-MRD: Showing NP-Card for 1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one (NP0193501)

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Record Information

Version

2.0

Created at

2022-09-04 10:57:28 UTC

Updated at

2022-09-04 10:57:28 UTC

NP-MRD ID

NP0193501

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one

Description

Uridine 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. It is one of the five standard nucleosides which make up nucleic acids, the others being adenosine, thymidine, cytidine and guanosine. However, thymidine is more commonly written as 'dT' ('d' represents 'deoxy') as it contains a 2'-deoxyribofuranose moiety rather than the ribofuranose ring found in uridine. Uridine is an extremely weak basic (essentially neutral) compound (based on its pKa). In humans, uridine is involved in the metabolic disorder called the g(m2)-gangliosidosis: Variant b, tay-sachs disease pathway. Therefore, galactose is converted to glucose and metabolized in the common glucose pathway. Outside of the human body, Uridine is found, on average, in the highest concentration within milk (cow). Uridine has also been detected, but not quantified in, several different foods, such as chinese chives, biscuits, yellow wax beans, swamp cabbages, and root vegetables. This could make uridine a potential biomarker for the consumption of these foods. Uridine plays a role in the glycolysis pathway of galactose. This process is continued to allow the proper glycolysis of galactose. Some foods that contain uridine in the form of RNA are listed below. There is no catabolic process to metabolize galactose. Uridine is regarded as a non-essential nutrient, as it is produced by the human body as needed and supplementation is not generally recommended, though it has been explored for specific applications. The orotidylate is produced from orotate, which is combined with 5-phosphoribosyl-1-pyrophosphate (PRPP) to form orotidylate by pyrimidine phosphoribosyltransferase. 1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one is found in Alangium kurzii, Annona cherimola, Atractylodes lancea, Chrysanthemum zawadskii, Cistanche tubulosa, Dimocarpus longan, Eunicella cavolini, Garcinia dulcis, Gastrodia elata, Glehnia littoralis, Isatis tinctoria, Isodictya erinacea, Lepidium meyenii, Lepisorus contortus, Lindackeria dentata, Maytenus hookeri, Peucedanum japonicum, Prunus dulcis, Salsola collina, Sauropus androgynus, Spiraea formosana and Ulva pertusa. The end result is UDP-galactose and glucose-1-phosphate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652310061716302D          

 17 18  0  0  0  0            999 V2000
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3748    0.5154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
 10  5  2  0  0  0  0
 10  9  1  0  0  0  0
 11  2  1  0  0  0  0
 11  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  3  1  0  0  0  0
 13  5  1  0  0  0  0
 14  6  1  0  0  0  0
 15  7  1  0  0  0  0
 16  9  2  0  0  0  0
 17  4  1  0  0  0  0
 17  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0193501

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(C(O)C1O)N1C=CC(O)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)

> <INCHI_KEY>
DRTQHJPVMGBUCF-UHFFFAOYSA-N

> <FORMULA>
C9H12N2O6

> <MOLECULAR_WEIGHT>
244.2014

> <EXACT_MASS>
244.069536126

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
21.82875705473748

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.93

> <JCHEM_LOGP>
-2.047741337333334

> <ALOGPS_LOGS>
-0.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.553247165416206

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.480089429781644

> <JCHEM_PKA_STRONGEST_BASIC>
-2.98029983295402

> <JCHEM_POLAR_SURFACE_AREA>
122.82000000000001

> <JCHEM_REFRACTIVITY>
52.887299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.36e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-OCT-17         0                                  
HETATM    1  C   UNK     0       3.182  -6.383   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.087  -5.138   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.846  -0.544   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.381  -1.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.650  -6.222   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.366  -2.485   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.929  -3.570   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       1.024  -4.816   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       3.460  -3.731   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       8.166   0.962   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.745  -7.468   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       5.136   1.425   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.425  -0.544   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.302  -2.163   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       5.906  -2.485   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1   11                                                       
CONECT    3    4   12                                                       
CONECT    4    3    6   17                                                  
CONECT    5    1   10   13                                                  
CONECT    6    4    7   14                                                  
CONECT    7    6    8   15                                                  
CONECT    8    7   11   17                                                  
CONECT    9   10   11   16                                                  
CONECT   10    5    9                                                       
CONECT   11    2    8    9                                                  
CONECT   12    3                                                            
CONECT   13    5                                                            
CONECT   14    6                                                            
CONECT   15    7                                                            
CONECT   16    9                                                            
CONECT   17    4    8                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Value	Source
Ara-u	MeSH
Arabinofuranoside, uracil	MeSH
Arabinosyluracil	MeSH
Sponguridine	MeSH
Uracil arabinofuranoside	MeSH
1 beta D Arabinofuranosyl uracil	MeSH
Arabinofuranosyluracil	MeSH
Arauridine	MeSH
1-beta-D-Arabinofuranosyl uracil	MeSH
Ara u	MeSH
Arabinoside, uracil	MeSH
Uracil arabinoside	MeSH
Uracil, 1-beta-D-arabinofuranosyl	MeSH

Chemical Formula

C₉H₁₂N₂O₆

Average Mass

244.2014 Da

Monoisotopic Mass

244.06954 Da

IUPAC Name

1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,2-dihydropyrimidin-2-one

Traditional Name

1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one

CAS Registry Number

Not Available

SMILES

OCC1OC(C(O)C1O)N1C=CC(O)=NC1=O

InChI Identifier

InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)

InChI Key

DRTQHJPVMGBUCF-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 25.16 MHz, D₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Alangium kurzii	LOTUS Database	35616633
Annona cherimola	LOTUS Database	35616633
Atractylodes lancea	LOTUS Database	35616633
Chrysanthemum zawadskii	LOTUS Database	35616633
Cistanche tubulosa	LOTUS Database	35616633
Dimocarpus longan	LOTUS Database	35616633
Eunicella cavolini	LOTUS Database	35616633
Garcinia dulcis	LOTUS Database	35616633
Gastrodia elata	LOTUS Database	35616633
Glehnia littoralis	LOTUS Database	35616633
Isatis tinctoria	LOTUS Database	35616633
Isodictya erinacea	LOTUS Database	35616633
Lepidium meyenii	LOTUS Database	35616633
Lepisorus contortus	LOTUS Database	35616633
Lindackeria dentata	LOTUS Database	35616633
Maytenus hookeri	LOTUS Database	35616633
Peucedanum japonicum	LOTUS Database	35616633
Prunus dulcis	LOTUS Database	35616633
Salsola collina	LOTUS Database	35616633
Sauropus androgynus	LOTUS Database	35616633
Spiraea formosana	LOTUS Database	35616633
Ulva pertusa	LOTUS Database	35616633

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
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Vinylogous amide
Tetrahydrofuran
Heteroaromatic compound
Urea
Secondary alcohol
Lactam
Organoheterocyclic compound
Oxacycle
Azacycle
Hydrocarbon derivative
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Primary alcohol
Alcohol
Organic oxygen compound
Organic oxide
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a pyrimidine ribonucleoside (URIDINE )

Physical Properties

State

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
logP	-1.9	ALOGPS
logP	-2	ChemAxon
logS	-0.66	ALOGPS
pKa (Strongest Acidic)	7.48	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	122.82 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.89 m³·mol⁻¹	ChemAxon
Polarizability	21.83 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

FoodDB ID

FDB007411

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Uridine

METLIN ID

Not Available

PubChem Compound

1177

PDB ID

Not Available

ChEBI ID

143353

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one (NP0193501)

MOL for NP0193501 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

3D MOL for NP0193501 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

3D SDF for NP0193501 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

3D-SDF for NP0193501 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

PDB for NP0193501 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

3D PDB for NP0193501 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

SMILES for NP0193501 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

INCHI for NP0193501 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

Structure for NP0193501 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

3D Structure for NP0193501 (1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)