MiMeDB: Showing metabocard for Uridine 3',5'-phosphate (MMDBc0057213)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-11-10 16:35:42 UTC

Update Date

2025-10-07 16:09:57 UTC

Metabolite ID

MMDBc0057213

Metabolite Identification

Common Name

Uridine 3',5'-phosphate

Description

Uridine 3',5'-phosphate is a cyclic nucleotide belonging to the class of phosphates, specifically a cyclic nucleotide phosphate. Its chemical structure features a uridine base linked to a phosphate group through a phosphodiester bond, forming a cyclic arrangement that is crucial for its biological activity. This compound plays a role in various cellular signaling pathways, particularly those involving the regulation of phosphodiesterases, which are enzymes that hydrolyze cyclic nucleotides. For instance, a cyclic 3',5'-nucleotide phosphodiesterase has been identified in the heart that exhibits specificity for uridine 3',5'-phosphate, highlighting its importance in cardiac function and signaling (PMID:4284419 ). The cyclic nature of uridine 3',5'-phosphate allows it to participate in the modulation of intracellular processes, influencing various physiological responses. Its involvement in these pathways underscores the significance of cyclic nucleotides in cellular communication and regulation.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05041412312D          

 29 30  0  0  1  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  2  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
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  2  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
    0.3990   -4.0009    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
    6.3856   -0.3337    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559   -1.3733    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3460    0.1959    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8781    0.4614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0531    1.8904    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1801    1.5884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8163   -0.8436    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
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6010   -0.5887    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    1.1759    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.2612    0.2633    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9547    0.2683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3138    0.5418    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5238   -1.2021    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  1  0  0  0
  5  1  1  0  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  6  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
  8 11  1  1  0  0  0
 11  9  1  0  0  0  0
 12  5  1  0  0  0  0
  6 13  1  6  0  0  0
 14  9  2  0  0  0  0
 21  3  1  0  0  0  0
 22  4  1  0  0  0  0
 22  8  1  0  0  0  0
  7 23  1  6  0  0  0
 24 15  1  0  0  0  0
 24 16  1  0  0  0  0
 24 17  2  0  0  0  0
 24 21  1  0  0  0  0
 25 18  1  0  0  0  0
 25 19  1  0  0  0  0
 25 20  2  0  0  0  0
 25 23  1  0  0  0  0
  4 26  1  6  0  0  0
  6 27  1  1  0  0  0
  7 28  1  1  0  0  0
  8 29  1  6  0  0  0
M  END


  Mrv0541 05041412312D          

 29 30  0  0  1  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  2  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
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  2  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
    0.3990   -4.0009    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
    6.3856   -0.3337    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559   -1.3733    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3460    0.1959    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8781    0.4614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0531    1.8904    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1801    1.5884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8163   -0.8436    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
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6010   -0.5887    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    1.1759    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.2612    0.2633    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9547    0.2683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3138    0.5418    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5238   -1.2021    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  1  0  0  0
  5  1  1  0  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  6  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
  8 11  1  1  0  0  0
 11  9  1  0  0  0  0
 12  5  1  0  0  0  0
  6 13  1  6  0  0  0
 14  9  2  0  0  0  0
 21  3  1  0  0  0  0
 22  4  1  0  0  0  0
 22  8  1  0  0  0  0
  7 23  1  6  0  0  0
 24 15  1  0  0  0  0
 24 16  1  0  0  0  0
 24 17  2  0  0  0  0
 24 21  1  0  0  0  0
 25 18  1  0  0  0  0
 25 19  1  0  0  0  0
 25 20  2  0  0  0  0
 25 23  1  0  0  0  0
  4 26  1  6  0  0  0
  6 27  1  1  0  0  0
  7 28  1  1  0  0  0
  8 29  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057213

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP(O)(O)=O)O[C@@]([H])(N2C=CC(O)=NC2=O)[C@]([H])(O)[C@]1([H])OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(14)10-5)8-6(13)7(23-25(18,19)20)4(22-8)3-21-24(15,16)17/h1-2,4,6-8,13H,3H2,(H,10,12,14)(H2,15,16,17)(H2,18,19,20)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
ZPVPRWPOZBXDKD-XVFCMESISA-N

> <FORMULA>
C9H14N2O12P2

> <MOLECULAR_WEIGHT>
404.1612

> <EXACT_MASS>
404.002196946

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
31.159840581006737

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-4-hydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)-2-[(phosphonooxy)methyl]oxolan-3-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-0.89

> <JCHEM_LOGP>
-2.2948734

> <ALOGPS_LOGS>
-1.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.3845527438576202

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.7111506735408284

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8088171645695708

> <JCHEM_POLAR_SURFACE_AREA>
215.87999999999994

> <JCHEM_REFRACTIVITY>
74.63309999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.08e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-4-hydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)-2-[(phosphonooxy)methyl]oxolan-3-yl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   24  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   25  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   26  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   29  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    5                                                       
CONECT    2    1   11                                                       
CONECT    3    4   21                                                       
CONECT    4    3    7   22   26                                             
CONECT    5    1   10   12                                                  
CONECT    6    7    8   13   27                                             
CONECT    7    4    6   23   28                                             
CONECT    8    6   11   22   29                                             
CONECT    9   10   11   14                                                  
CONECT   10    5    9                                                       
CONECT   11    2    8    9                                                  
CONECT   12    5                                                            
CONECT   13    6                                                            
CONECT   14    9                                                            
CONECT   15   24                                                            
CONECT   16   24                                                            
CONECT   17   24                                                            
CONECT   18   25                                                            
CONECT   19   25                                                            
CONECT   20   25                                                            
CONECT   21    3   24                                                       
CONECT   22    4    8                                                       
CONECT   23    7   25                                                       
CONECT   24   15   16   17   21                                             
CONECT   25   18   19   20   23                                             
CONECT   26    4                                                            
CONECT   27    6                                                            
CONECT   28    7                                                            
CONECT   29    8                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   60    0
END

Synonyms

Value	Source
Uridine 3',5'-bis(dihydrogen phosphoric acid)	Generator
{[(2R,3S,4R,5R)-4-hydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)-3-(phosphonooxy)oxolan-2-yl]methoxy}phosphonate	Generator

Molecular Formula

C₉H₁₄N₂O₁₂P₂

Average Mass

404.1612

Monoisotopic Mass

404.002196946

IUPAC Name

{[(2R,3S,4R,5R)-4-hydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)-2-[(phosphonooxy)methyl]oxolan-3-yl]oxy}phosphonic acid

Traditional Name

[(2R,3S,4R,5R)-4-hydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)-2-[(phosphonooxy)methyl]oxolan-3-yl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP(O)(O)=O)O[C@@]([H])(N2C=CC(O)=NC2=O)[C@]([H])(O)[C@]1([H])OP(O)(O)=O

InChI Identifier

InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(14)10-5)8-6(13)7(23-25(18,19)20)4(22-8)3-21-24(15,16)17/h1-2,4,6-8,13H,3H2,(H,10,12,14)(H2,15,16,17)(H2,18,19,20)/t4-,6-,7-,8-/m1/s1

InChI Key

ZPVPRWPOZBXDKD-XVFCMESISA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	10.8 g/L	ALOGPS
logP	-0.89	ALOGPS
logP	-2.3	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	0.71	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	215.88 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	74.63 m³·mol⁻¹	ChemAxon
Polarizability	31.16 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

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
MMDBr0026084	Uridine 3',5'-phosphate	Uridine 5'-monophosphate	5'-3' exoribonuclease	5S, 16S and 23S rRNA 5'-end maturation; Dephosphorylation	RHEA	34755880

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

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

54559969

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for Uridine 3',5'-phosphate (MMDBc0057213)

MOL for #<Metabolite:0x00007f8d923d05c8>

3D MOL for #<Metabolite:0x00007f8d923d05c8>

3D SDF for #<Metabolite:0x00007f8d923d05c8>

3D-SDF for #<Metabolite:0x00007f8d923d05c8>

PDB for #<Metabolite:0x00007f8d923d05c8>

3D PDB for #<Metabolite:0x00007f8d923d05c8>

SMILES for #<Metabolite:0x00007f8d923d05c8>

INCHI for #<Metabolite:0x00007f8d923d05c8>

Structure for #<Metabolite:0x00007f8d923d05c8>

3D Structure for #<Metabolite:0x00007f8d923d05c8>