MiMeDB: Showing metabocard for Deoxyuridine-5'-diphosphate (MMDBc0031893)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:53:48 UTC

Update Date

2022-08-31 18:25:48 UTC

Metabolite ID

MMDBc0031893

Metabolite Identification

Common Name

Deoxyuridine-5'-diphosphate

Description

Deoxyuridine-5'-diphosphate (also known as 2'-Deoxyuridine 5'-diphosphate or dUDP) is a metabolite involved in pyrimidine metabolism. In the pyrimidine metabolism pathway, dUDP is converted to dUTP by the ATP:dUDP phosphotransferase (EC 2.7.4.6) in E. coli.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231216552D          

 24 25  0  0  1  0            999 V2000
    1.4243   -4.9595    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8112   -4.4075    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0042   -4.5790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4083   -3.8645    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1437   -3.2514    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8974   -3.5870    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3264   -3.5870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0408   -3.1745    0.0000 P   0  0  2  0  0  0  0  0  0  0  0  0
    2.6283   -2.4600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4533   -3.8890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7553   -2.7620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4698   -3.1745    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.1842   -3.5870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8823   -2.4600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0573   -3.8890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2288   -3.7783    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7137   -4.4457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5342   -4.3595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8697   -3.6058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6902   -3.5196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3848   -2.9384    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5643   -3.0246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0794   -2.3572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  1  0  0  0  0
  9  8  1  1  0  0  0
  9 10  1  6  0  0  0
  9 11  2  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 13 16  2  0  0  0  0
  4 17  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 17 23  1  0  0  0  0
 23 24  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031893

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N2O11P2/c12-5-3-8(11-2-1-7(13)10-9(11)14)21-6(5)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,10,13,14)(H2,15,16,17)/t5-,6+,8-/m1/s1

> <INCHI_KEY>
QHWZTVCCBMIIKE-GKROBHDKSA-N

> <FORMULA>
C9H14N2O11P2

> <MOLECULAR_WEIGHT>
388.1618

> <EXACT_MASS>
388.007282324

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
30.232387024219406

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.99

> <JCHEM_LOGP>
-2.0599685889999995

> <ALOGPS_LOGS>
-1.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1904051655109784

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7717479360816935

> <JCHEM_PKA_STRONGEST_BASIC>
-3.240344155883659

> <JCHEM_POLAR_SURFACE_AREA>
192.16000000000003

> <JCHEM_REFRACTIVITY>
72.8007

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.03e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
deoxyuridine-5'-diphosphate

> <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       2.659  -9.258   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.514  -8.227   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.008  -8.547   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.762  -7.214   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.268  -6.069   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.675  -6.696   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.009  -5.926   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.343  -6.696   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0       5.676  -5.926   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0       4.906  -4.592   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.446  -7.259   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       7.010  -5.156   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0       8.344  -5.926   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0       9.677  -6.696   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       9.114  -4.592   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       7.574  -7.259   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0      -2.294  -7.053   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      -3.199  -8.299   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.731  -8.138   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.357  -6.731   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -6.888  -6.570   0.000  0.00  0.00           O+0
HETATM   22  N   UNK     0      -4.452  -5.485   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      -2.920  -5.646   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -2.015  -4.400   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   17                                                  
CONECT    5    4    6                                                       
CONECT    6    5    2    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9   13                                                       
CONECT   13   12   14   15   16                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   13                                                            
CONECT   17    4   18   23                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   17   24                                                  
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   50    0
END

Synonyms

Value	Source
Deoxyuridine-5'-diphosphoric acid	Generator

Molecular Formula

C₉H₁₄N₂O₁₁P₂

Average Mass

388.1618

Monoisotopic Mass

388.007282324

IUPAC Name

[({[(2S,3R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

deoxyuridine-5'-diphosphate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H14N2O11P2/c12-5-3-8(11-2-1-7(13)10-9(11)14)21-6(5)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,10,13,14)(H2,15,16,17)/t5-,6+,8-/m1/s1

InChI Key

QHWZTVCCBMIIKE-GKROBHDKSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine deoxyribonucleotides

Direct Parent

Pyrimidine 2'-deoxyribonucleoside diphosphates

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside diphosphate
Organic pyrophosphate
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Lactam
Urea
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
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	8.03 g/L	ALOGPS
logP	-0.99	ALOGPS
logP	-2.1	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	192.16 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	72.8 m³·mol⁻¹	ChemAxon
Polarizability	30.23 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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0026020	2'-Deoxyuridine 5'-phosphate	Deoxyuridine-5'-diphosphate	Deoxynucleotide monophosphate kinase	Phosphorylation	RHEA	34755880
MMDBr0026057	L-Cystine	L-Cysteine	Vitamin B12-dependent ribonucleoside-diphosphate reductase	Reduction	RHEA	34755880
MMDBr0026085	Deoxyuridine-5'-diphosphate	Deoxyuridine triphosphate	Nucleoside diphosphate kinase	Phosphorylation	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
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46936665

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 Deoxyuridine-5'-diphosphate (MMDBc0031893)

MOL for #<Metabolite:0x00007f92580c89f0>

3D MOL for #<Metabolite:0x00007f92580c89f0>

3D SDF for #<Metabolite:0x00007f92580c89f0>

3D-SDF for #<Metabolite:0x00007f92580c89f0>

PDB for #<Metabolite:0x00007f92580c89f0>

3D PDB for #<Metabolite:0x00007f92580c89f0>

SMILES for #<Metabolite:0x00007f92580c89f0>

INCHI for #<Metabolite:0x00007f92580c89f0>

Structure for #<Metabolite:0x00007f92580c89f0>

3D Structure for #<Metabolite:0x00007f92580c89f0>