MiMeDB: Showing metabocard for Pyrimidine nucleoside (MMDBc0031964)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:56:46 UTC

Update Date

2022-08-31 18:26:53 UTC

Metabolite ID

MMDBc0031964

Metabolite Identification

Common Name

Pyrimidine nucleoside

Description

NULL

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533007211515522D          
 
 15 16  0  0  1  0            999 V2000
   17.0069  -13.6249    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.4991  -12.5345    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   16.3343  -13.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7485  -14.4108    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.2212  -12.1167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7875  -12.1167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6758  -13.6249    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.9236  -14.4108    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.2371  -15.0728    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2212  -11.2812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7875  -11.2812    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.8934  -13.3663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.4351  -15.0728    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4991  -10.8741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7235  -12.5628    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  1  6  0  0  0
  5 10  2  0  0  0  0
  6 11  1  0  0  0  0
  7 12  1  1  0  0  0
  8 13  1  6  0  0  0
 10 14  1  0  0  0  0
 12 15  1  0  0  0  0
  7  8  1  0  0  0  0
 11 14  2  0  0  0  0
M  CHG  1   2   1
M  END
> <DATABASE_ID>
MMDBc0031964

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)[N+]1=CN=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N2O4/c12-4-6-7(13)8(14)9(15-6)11-3-1-2-10-5-11/h1-3,5-9,12-14H,4H2/q+1/t6-,7-,8-,9-/m1/s1

> <INCHI_KEY>
UAGYHIZGHDGMCY-FNCVBFRFSA-N

> <FORMULA>
C9H13N2O4

> <MOLECULAR_WEIGHT>
213.212

> <EXACT_MASS>
213.086983327

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
20.520681644513036

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1λ⁵-pyrimidin-1-ylium

> <ALOGPS_LOGP>
-2.83

> <JCHEM_LOGP>
-6.1697763138050785

> <ALOGPS_LOGS>
-0.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.658381598003473

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.720199727030138

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9841647658438717

> <JCHEM_POLAR_SURFACE_AREA>
86.69000000000001

> <JCHEM_REFRACTIVITY>
49.9521

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.16e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1λ⁵-pyrimidin-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 21-JUL-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-JUL-15         0                                  
HETATM    1  C   UNK     0      31.746 -25.433   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      32.665 -23.398   0.000  0.00  0.00           N+1
HETATM    3  O   UNK     0      30.491 -24.534   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      31.264 -26.900   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      34.013 -22.618   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      31.337 -22.618   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      29.262 -25.433   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      29.724 -26.900   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      32.176 -28.136   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      34.013 -21.058   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      31.337 -21.058   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      27.801 -24.950   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      28.812 -28.136   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      32.665 -20.298   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      27.484 -23.451   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8    9                                                  
CONECT    5    2   10                                                       
CONECT    6    2   11                                                       
CONECT    7    3   12    8                                                  
CONECT    8    4   13    7                                                  
CONECT    9    4                                                            
CONECT   10    5   14                                                       
CONECT   11    6   14                                                       
CONECT   12    7   15                                                       
CONECT   13    8                                                            
CONECT   14   10   11                                                       
CONECT   15   12                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

Synonyms

Value	Source
N-D-Ribosylpyrimidine	Kegg

Molecular Formula

C₉H₁₃N₂O₄

Average Mass

213.212

Monoisotopic Mass

213.086983327

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1λ⁵-pyrimidin-1-ylium

Traditional Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1λ⁵-pyrimidin-1-ylium

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)[N+]1=CN=CC=C1

InChI Identifier

InChI=1S/C9H13N2O4/c12-4-6-7(13)8(14)9(15-6)11-3-1-2-10-5-11/h1-3,5-9,12-14H,4H2/q+1/t6-,7-,8-,9-/m1/s1

InChI Key

UAGYHIZGHDGMCY-FNCVBFRFSA-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
Monosaccharide
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Alcohol
Primary alcohol
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organic cation
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	31.6 g/L	ALOGPS
logP	-2.8	ALOGPS
logP	-6.2	ChemAxon
logS	-0.9	ALOGPS
pKa (Strongest Acidic)	11.72	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.69 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	49.95 m³·mol⁻¹	ChemAxon
Polarizability	20.52 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

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C03169

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pyrimidine

METLIN ID

Not Available

PubChem Compound

439920

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Sajed T, Marcu A, Ramirez M, Pon A, Guo AC, Knox C, Wilson M, Grant JR, Djoumbou Y, Wishart DS: ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res. 2016 Jan 4;44(D1):D495-501. doi: 10.1093/nar/gkv1060. Epub 2015 Oct 19. [PubMed:26481353 ]

Showing metabocard for Pyrimidine nucleoside (MMDBc0031964)

MOL for #<Metabolite:0x0000560be2658490>

3D MOL for #<Metabolite:0x0000560be2658490>

3D SDF for #<Metabolite:0x0000560be2658490>

3D-SDF for #<Metabolite:0x0000560be2658490>

PDB for #<Metabolite:0x0000560be2658490>

3D PDB for #<Metabolite:0x0000560be2658490>

SMILES for #<Metabolite:0x0000560be2658490>

INCHI for #<Metabolite:0x0000560be2658490>

Structure for #<Metabolite:0x0000560be2658490>

3D Structure for #<Metabolite:0x0000560be2658490>