MiMeDB: Showing metabocard for 2'-Deoxyuridine 3'-phosphate (MMDBc0057211)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-11-10 16:35:27 UTC

Update Date

2022-11-10 16:35:27 UTC

Metabolite ID

MMDBc0057211

Metabolite Identification

Common Name

2'-Deoxyuridine 3'-phosphate

Description

2'-Deoxyuridine 3'-Monophosphate, also known as 3'-dUMP, belongs to the class of organic compounds known as ribonucleoside 3'-phosphates. These are ribonucleosides that contain a phosphate group attached to the C-3 carbon of the ribose or deoxyribose moiety. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives. 2'-Deoxyuridine 3'-Monophosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). A pyrimidine 2'-deoxyribonucleoside 3'-monophosphate having uracil as the nucleobase.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231216562D          

 20 21  0  0  1  0            999 V2000
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9091   -0.6605    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0806    0.1465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7161   -0.8320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1021   -0.4890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4324   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9173   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5817   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667   -5.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7613   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4559   -4.0144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  2  0  0  0  0
  5 13  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 13 19  1  0  0  0  0
 19 20  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057211

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1O[C@H](C[C@@H]1OP(O)(O)=O)N1C=CC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N2O8P/c12-4-6-5(19-20(15,16)17)3-8(18-6)11-2-1-7(13)10-9(11)14/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

> <INCHI_KEY>
LXKGKXYIAAKOCT-SHYZEUOFSA-N

> <FORMULA>
C9H13N2O8P

> <MOLECULAR_WEIGHT>
308.1819

> <EXACT_MASS>
308.040951914

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
25.626367887769536

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-2-(hydroxymethyl)oxolan-3-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-1.55

> <JCHEM_LOGP>
-1.6381701099999995

> <ALOGPS_LOGS>
-1.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.122364501357099

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0934221737510303

> <JCHEM_PKA_STRONGEST_BASIC>
-2.979075857529735

> <JCHEM_POLAR_SURFACE_AREA>
145.63

> <JCHEM_REFRACTIVITY>
61.92779999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.41e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3'-dUMP

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.580  -3.215   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.377  -2.739   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0      -1.697  -1.233   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0      -2.017   0.273   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -3.203  -1.553   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -0.191  -0.913   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0       3.009  -5.926   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       4.540  -5.765   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.446  -7.011   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.819  -8.418   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       5.725  -9.663   0.000  0.00  0.00           O+0
HETATM   18  N   UNK     0       3.288  -8.578   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       2.382  -7.333   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       0.851  -7.494   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   13                                                  
CONECT    6    5    7                                                       
CONECT    7    6    3    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13    5   14   19                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   13   20                                                  
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

Synonyms

Value	Source
3'-dUMP	ChEBI
2'-Deoxyuridine 3'-monophosphoric acid	Generator

Molecular Formula

C₉H₁₃N₂O₈P

Average Mass

308.1819

Monoisotopic Mass

308.040951914

IUPAC Name

{[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-2-(hydroxymethyl)oxolan-3-yl]oxy}phosphonic acid

Traditional Name

3'-dUMP

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H](C[C@@H]1OP(O)(O)=O)N1C=CC(=O)NC1=O

InChI Identifier

InChI=1S/C9H13N2O8P/c12-4-6-5(19-20(15,16)17)3-8(18-6)11-2-1-7(13)10-9(11)14/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

InChI Key

LXKGKXYIAAKOCT-SHYZEUOFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ribonucleoside 3'-phosphates. These are ribonucleosides that contain a phosphate group attached to the C-3 carbon of the ribose or deoxyribose moiety. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Ribonucleoside 3'-phosphates

Sub Class

Not Available

Direct Parent

Ribonucleoside 3'-phosphates

Alternative Parents

Substituents

Ribonucleoside 3'-phosphate
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Tetrahydrofuran
Heteroaromatic compound
Vinylogous amide
Urea
Lactam
Oxacycle
Organoheterocyclic compound
Azacycle
Alcohol
Hydrocarbon derivative
Organic oxide
Primary alcohol
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside 3'-monophosphate (CHEBI:46322 )
deoxyuridine phosphate (CHEBI:46322 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	8.41 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-1.6	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.09	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	145.63 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	61.93 m³·mol⁻¹	ChemAxon
Polarizability	25.63 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9320000000-f31cc30d6769431763f0	2017-08-28	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1900000000-2dac39d45011ae927b18	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-5900000000-c785a03f5384fbb2bdb5	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-8900000000-e430d8a001c5749847db	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-06tf-9163000000-f56a7173cc150fa1eb36	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004l-9120000000-a900ed4aff3f8650c860	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a42503b4fe3866cfdbae	2017-07-26	View Spectrum

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

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

Exposure Sources

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

DB03448

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

449392

PDB ID

Not Available

ChEBI ID

46322

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 2'-Deoxyuridine 3'-phosphate (MMDBc0057211)

MOL for #<Metabolite:0x00007fdb48011cf8>

3D MOL for #<Metabolite:0x00007fdb48011cf8>

3D SDF for #<Metabolite:0x00007fdb48011cf8>

3D-SDF for #<Metabolite:0x00007fdb48011cf8>

PDB for #<Metabolite:0x00007fdb48011cf8>

3D PDB for #<Metabolite:0x00007fdb48011cf8>

SMILES for #<Metabolite:0x00007fdb48011cf8>

INCHI for #<Metabolite:0x00007fdb48011cf8>

Structure for #<Metabolite:0x00007fdb48011cf8>

3D Structure for #<Metabolite:0x00007fdb48011cf8>