MiMeDB: Showing metabocard for 5,6-Dihydrouridine 5'-monophosphate (MMDBc0057143)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-11-09 19:14:07 UTC

Update Date

2022-11-09 19:14:07 UTC

Metabolite ID

MMDBc0057143

Metabolite Identification

Common Name

5,6-Dihydrouridine 5'-monophosphate

Description

5,6-dihydrouridine 5'-monophosphate, also known as 5,6-dihydro-5'-uridylic acid or 5,6-dihydro-UMP, belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety. A uridine 5'-phosphate that is the 5,6-dihydro derivative of uridine 5'-monophosphate. 5,6-dihydrouridine 5'-monophosphate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05041402442D          

 25 26  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
    2.7512   -0.0616    0.0000 C   0  0  2  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
    2.3387   -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
    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
    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
    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
    5.6010   -0.5887    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
    3.3138    0.5418    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
    1.5238   -1.2021    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  1  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  1  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  2  0  0  0  0
  6 13  1  6  0  0  0
  7 14  1  6  0  0  0
 15  9  2  0  0  0  0
 19  3  1  0  0  0  0
 20  4  1  0  0  0  0
 20  8  1  0  0  0  0
 21 16  1  0  0  0  0
 21 17  1  0  0  0  0
 21 18  2  0  0  0  0
 21 19  1  0  0  0  0
  4 22  1  6  0  0  0
  6 23  1  1  0  0  0
  7 24  1  1  0  0  0
  8 25  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057143

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP(O)(O)=O)O[C@@]([H])(N2CCC(=O)NC2=O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C9H15N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h4,6-8,13-14H,1-3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
NBWDKGJHOHJBRJ-XVFCMESISA-N

> <FORMULA>
C9H15N2O9P

> <MOLECULAR_WEIGHT>
326.1972

> <EXACT_MASS>
326.0515166

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
26.767611512405555

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-(2,4-dioxo-1,3-diazinan-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-1.81

> <JCHEM_LOGP>
-2.8967249043333334

> <ALOGPS_LOGS>
-1.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.2513606403899

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.225543829304229

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6642706453728486

> <JCHEM_POLAR_SURFACE_AREA>
165.85999999999999

> <JCHEM_REFRACTIVITY>
63.2147

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.47e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-5-(2,4-dioxo-1,3-diazinan-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxyphosphonic 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  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   22  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   25  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   19                                                       
CONECT    4    3    6   20   22                                             
CONECT    5    1   10   12                                                  
CONECT    6    4    7   13   23                                             
CONECT    7    6    8   14   24                                             
CONECT    8    7   11   20   25                                             
CONECT    9   10   11   15                                                  
CONECT   10    5    9                                                       
CONECT   11    2    8    9                                                  
CONECT   12    5                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    9                                                            
CONECT   16   21                                                            
CONECT   17   21                                                            
CONECT   18   21                                                            
CONECT   19    3   21                                                       
CONECT   20    4    8                                                       
CONECT   21   16   17   18   19                                             
CONECT   22    4                                                            
CONECT   23    6                                                            
CONECT   24    7                                                            
CONECT   25    8                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

Synonyms

Value	Source
2,4-Dioxotetrahydropyrimidine D-ribonucleotide	ChEBI
5,6-Dihydro-5'-uridylic acid	ChEBI
5,6-Dihydro-UMP	ChEBI
5,6-Dihydro-5'-uridylate	Generator
5,6-Dihydrouridine 5'-monophosphoric acid	Generator

Molecular Formula

C₉H₁₅N₂O₉P

Average Mass

326.1972

Monoisotopic Mass

326.0515166

IUPAC Name

{[(2R,3S,4R,5R)-5-(2,4-dioxo-1,3-diazinan-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

[(2R,3S,4R,5R)-5-(2,4-dioxo-1,3-diazinan-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP(O)(O)=O)O[C@@]([H])(N2CCC(=O)NC2=O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C9H15N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h4,6-8,13-14H,1-3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

InChI Key

NBWDKGJHOHJBRJ-XVFCMESISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside monophosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Pentose monosaccharide
Monoalkyl phosphate
Ureide
N-acyl urea
Pyrimidone
Monosaccharide
Alkyl phosphate
Organic phosphoric acid derivative
Pyrimidine
Phosphoric acid ester
1,3-diazinane
Tetrahydrofuran
Dicarboximide
Urea
Carbonic acid derivative
Secondary alcohol
1,2-diol
Organoheterocyclic compound
Oxacycle
Azacycle
Carboxylic acid derivative
Hydrocarbon derivative
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organopnictogen compound
Organic oxide
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

uridine 5'-phosphate (CHEBI:74673 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	14.7 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.9	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	165.86 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	63.21 m³·mol⁻¹	ChemAxon
Polarizability	26.77 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

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

Metabolic Reactions

Not Available

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

Source Type	Source Sub-type	Species	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

C04639

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440416

PDB ID

Not Available

ChEBI ID

74673

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 5,6-Dihydrouridine 5'-monophosphate (MMDBc0057143)

MOL for #<Metabolite:0x00007fecc93f41d0>

3D MOL for #<Metabolite:0x00007fecc93f41d0>

3D SDF for #<Metabolite:0x00007fecc93f41d0>

3D-SDF for #<Metabolite:0x00007fecc93f41d0>

PDB for #<Metabolite:0x00007fecc93f41d0>

3D PDB for #<Metabolite:0x00007fecc93f41d0>

SMILES for #<Metabolite:0x00007fecc93f41d0>

INCHI for #<Metabolite:0x00007fecc93f41d0>

Structure for #<Metabolite:0x00007fecc93f41d0>

3D Structure for #<Metabolite:0x00007fecc93f41d0>