NP-MRD: Showing NP-Card for dTDP (NP0044268)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-02-14 20:40:21 UTC

Updated at

2022-03-10 22:20:35 UTC

NP-MRD ID

NP0044268

Secondary Accession Numbers

None

Natural Product Identification

Common Name

dTDP

Description

DTDP, also known as deoxy-TDP, 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. DTDP is an extremely weak basic (essentially neutral) compound (based on its pKa). DTDP exists in all living species, ranging from bacteria to humans. Outside of the human body, dTDP has been detected, but not quantified in, several different foods, such as brussel sprouts, wheats, herbs and spices, papaya, and red raspberries. This could make dTDP a potential biomarker for the consumption of these foods. A thymidine phosphate having a diphosphate group at the 5'-position. DTDP is expected to be in Cannabis as all living plants are known to produce and metabolize it.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 41 42  0  0  0  0  0  0  0  0999 V2000
   -5.1046    2.3905   -0.6253 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5736    1.1604    0.0185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2273    0.9681    0.2766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7532   -0.1433    0.8576 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3534   -0.2648    1.0891 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8479   -1.6499    1.3207 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6587   -1.4439    1.1289 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2629   -1.2391    2.3648 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6924   -0.1718    0.2995 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6062   -0.3302   -0.8873 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9029   -0.6253   -0.5180 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9377   -0.8061   -1.8146 P   0  0  1  0  0  5  0  0  0  0  0  0
    5.1453   -1.6332   -1.4972 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1035   -1.5725   -3.0677 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4798    0.7324   -2.2997 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3664    1.3991   -1.0244 P   0  0  2  0  0  5  0  0  0  0  0  0
    4.4382    2.2342   -0.1471 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5809    2.4398   -1.6180 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0013    0.1790   -0.0747 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6006    0.1219   -0.0444 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6366   -1.0976    1.1956 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2114   -2.1353    1.7359 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9710   -0.9353    0.9530 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4658    0.1710    0.3718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7040    0.2643    0.1737 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3238    2.8118   -1.2966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3830    3.0919    0.1887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9964    2.2109   -1.2251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5396    1.7579   -0.0086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9852    0.3716    1.9290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9657   -2.0176    2.3551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2108   -2.3687    0.5525 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1213   -2.2987    0.6008 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8313   -0.4329    2.2792 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0911    0.6912    0.8960 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6389    0.6696   -1.3943 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1928   -1.0291   -1.6434 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4431   -2.2264   -2.7222 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3801    1.8505   -1.7648 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6256    0.5890    0.5943 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6462   -1.6837    1.2202 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 12 11  1  1
 12 14  1  0
 12 13  2  0
 12 15  1  0
 16 15  1  6
 16 18  1  0
 16 19  1  0
 16 17  2  0
  9 20  1  0
  4 21  1  0
 21 22  2  0
 21 23  1  0
 23 24  1  0
 24 25  2  0
 24  2  1  0
 20  5  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  5 30  1  1
  6 31  1  0
  6 32  1  0
  7 33  1  6
  8 34  1  0
  9 35  1  1
 10 36  1  0
 10 37  1  0
 14 38  1  0
 18 39  1  0
 19 40  1  0
 23 41  1  0
M  END


  Mrv1652309042000202D          

 25 26  0  0  1  0            999 V2000
    1.2169    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0040    0.2613    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5741    0.4744    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9728   -0.8044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6227   -0.2888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1759    1.0656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997   -0.0171    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1478   -0.8044    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4133   -0.0309    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4612   -1.0965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9562    1.3303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8834    0.2372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3403   -1.4678    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5818    0.7803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1178    2.1381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4953   -0.3128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3655    1.0346    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3168   -0.3128    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1418   -0.3128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3237   -1.1378    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3237    0.5087    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9634   -0.3093    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9668   -1.1343    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7849   -0.3093    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9668    0.5122    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  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5  9  1  0  0  0  0
  5 10  2  0  0  0  0
  6 11  2  0  0  0  0
  7 12  1  1  0  0  0
  8 13  1  6  0  0  0
  9 14  1  0  0  0  0
 11 15  1  0  0  0  0
 12 16  1  0  0  0  0
 14 17  2  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  2  0  0  0  0
 19 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 22 25  2  0  0  0  0
  7  8  1  0  0  0  0
 11 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0044268

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1

> <INCHI_KEY>
UJLXYODCHAELLY-XLPZGREQSA-N

> <FORMULA>
C10H16N2O11P2

> <MOLECULAR_WEIGHT>
402.1884

> <EXACT_MASS>
402.022932388

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
32.12109849726626

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.87

> <JCHEM_LOGP>
-1.6644180996666658

> <ALOGPS_LOGS>
-1.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.210405220777684

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7717480097137095

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2403442590936775

> <JCHEM_POLAR_SURFACE_AREA>
192.15999999999997

> <JCHEM_REFRACTIVITY>
77.1578

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.94e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dTDP

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       2.272   0.000   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       3.741   0.488   0.000  0.00  0.00           N+0
HETATM    3  O   UNK     0       1.072   0.886   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.816  -1.502   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.896  -0.539   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.062   1.989   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.186  -0.032   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.276  -1.502   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       6.371  -0.058   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       4.594  -2.047   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.518   2.483   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.649   0.443   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.635  -2.740   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.686   1.457   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.820   3.991   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.791  -0.584   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       8.149   1.931   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0      -4.325  -0.584   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0      -5.865  -0.584   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -4.338  -2.124   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -4.338   0.950   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0      -7.398  -0.577   0.000  0.00  0.00           P+0
HETATM   23  O   UNK     0      -7.405  -2.117   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -8.932  -0.577   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -7.405   0.956   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                                                       
CONECT    5    2    9   10                                                  
CONECT    6    2   11                                                       
CONECT    7    3   12    8                                                  
CONECT    8    4   13    7                                                  
CONECT    9    5   14                                                       
CONECT   10    5                                                            
CONECT   11    6   15   14                                                  
CONECT   12    7   16                                                       
CONECT   13    8                                                            
CONECT   14    9   17   11                                                  
CONECT   15   11                                                            
CONECT   16   12   18                                                       
CONECT   17   14                                                            
CONECT   18   16   19   20   21                                             
CONECT   19   18   22                                                       
CONECT   20   18                                                            
CONECT   21   18                                                            
CONECT   22   19   23   24   25                                             
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   22                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

View in JSmol

Synonyms

Value	Source
2'-Deoxyribosylthymine 5'-(trihydrogen diphosphate)	ChEBI
Deoxy-TDP	ChEBI
Deoxythymidine 5'-diphosphate	ChEBI
Thymidine 5'-diphosphate	ChEBI
Thymidine 5'-pyrophosphate	ChEBI
THYMIDINE-5'- diphosphATE	ChEBI
2'-Deoxyribosylthymine 5'-(trihydrogen diphosphoric acid)	Generator
Deoxythymidine 5'-diphosphoric acid	Generator
Thymidine 5'-diphosphoric acid	Generator
Thymidine 5'-pyrophosphoric acid	Generator
THYMIDINE-5'- diphosphoric acid	Generator
TDP	HMDB

Chemical Formula

C₁₀H₁₆N₂O₁₁P₂

Average Mass

402.1884 Da

Monoisotopic Mass

402.02293 Da

IUPAC Name

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

Traditional Name

dTDP

CAS Registry Number

491-97-4

SMILES

CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)NC1=O

InChI Identifier

InChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1

InChI Key

UJLXYODCHAELLY-XLPZGREQSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Abelmoschus esculentus	FooDB	FooDB
Actinidia chinensis	FooDB	FooDB
Agaricus bisporus	FooDB	FooDB
Agave	FooDB	FooDB
Allium ampeloprasum	FooDB	FooDB
Allium ascalonicum	FooDB	FooDB
Allium cepa	FooDB	FooDB
Allium cepa L.	FooDB	FooDB
Allium fistulosum	FooDB	FooDB
Allium sativum	FooDB	FooDB
Allium schoenoprasum	FooDB	FooDB
Allium tuberosum	FooDB	FooDB
Aloysia triphylla	FooDB	FooDB
Amaranthus	FooDB	FooDB
Amelanchier alnifolia	FooDB	FooDB
Anacardium occidentale	FooDB	FooDB
Ananas comosus	FooDB	FooDB
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anethum graveolens	FooDB	FooDB
Angelica keiskei	FooDB	FooDB
Annona cherimola	FooDB	FooDB
Annona muricata	FooDB	FooDB
Annona reticulata	FooDB	FooDB
Annona squamosa	FooDB	FooDB
Anser anser	FooDB	FooDB
Anthriscus cerefolium	FooDB	FooDB
Apium graveolens	FooDB	FooDB
Apium graveolens var. dulce	FooDB	FooDB
Apium graveolens var. rapaceum	FooDB	FooDB
Apium graveolens var. secalinum	FooDB	FooDB
Arachis hypogaea	FooDB	FooDB
Arctium lappa	FooDB	FooDB
Armoracia rusticana	FooDB	FooDB
Artemisia dracunculus	FooDB	FooDB
Artemisia vulgaris	FooDB	FooDB
Artocarpus altilis	FooDB	FooDB
Artocarpus heterophyllus	FooDB	FooDB
Asparagus officinalis	FooDB	FooDB
Attalea speciosa	FooDB	FooDB
Auricularia auricula-judae	FooDB	FooDB
Auricularia polytricha	FooDB	FooDB
Avena sativa L.	FooDB	FooDB
Averrhoa carambola	FooDB	FooDB
Basella alba	FooDB	FooDB
Benincasa hispida	FooDB	FooDB
Bertholletia excelsa	FooDB	FooDB
Beta vulgaris	FooDB	FooDB
Beta vulgaris ssp. cicla	FooDB	FooDB
Bison bison	FooDB	FooDB
Borago officinalis	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Brassica alboglabra	FooDB	FooDB
Brassica juncea	FooDB	FooDB
Brassica napus	FooDB	FooDB
Brassica napus var. napus	FooDB	FooDB
Brassica oleracea	FooDB	FooDB
Brassica oleracea var. botrytis	FooDB	FooDB
Brassica oleracea var. capitata	FooDB	FooDB
Brassica oleracea var. gemmifera	FooDB	FooDB
Brassica oleracea var. gongylodes	FooDB	FooDB
Brassica oleracea var. italica	FooDB	FooDB
Brassica oleracea var. sabauda	FooDB	FooDB
Brassica oleracea var. viridis	FooDB	FooDB
Brassica rapa	FooDB	FooDB
Brassica rapa ssp. chinensis	FooDB	FooDB
Brassica rapa var. pekinensis	FooDB	FooDB
Brassica rapa var. rapa	FooDB	FooDB
Brassica ruvo	FooDB	FooDB
Brosimum alicastrum	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Byrsonima crassifolia	FooDB	FooDB
Cajanus cajan	FooDB	FooDB
Canarium ovatum	FooDB	FooDB
Cannabis sativa	CannabisDB	Not Available
Cantharellus cibarius	FooDB	FooDB
Capparis spinosa	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Capsicum annuum	FooDB	FooDB
Capsicum annuum L.	FooDB	FooDB
Capsicum annuum var. annuum	FooDB	FooDB
Capsicum chinense	FooDB	FooDB
Capsicum pubescens	FooDB	FooDB
Carica papaya L.	FooDB	FooDB
Carissa macrocarpa	FooDB	FooDB
Carthamus tinctorius	FooDB	FooDB
Carum carvi	FooDB	FooDB
Carya	FooDB	FooDB
Carya illinoinensis	FooDB	FooDB
Castanea	FooDB	FooDB
Castanea crenata	FooDB	FooDB
Castanea mollissima	FooDB	FooDB
Castanea sativa	FooDB	FooDB
Ceratonia siliqua	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Chamaemelum nobile	FooDB	FooDB
Chamerion angustifolium	FooDB	FooDB
Chenopodium album	FooDB	FooDB
Chenopodium quinoa	FooDB	FooDB
Chrysanthemum coronarium	FooDB	FooDB
Cicer arietinum	FooDB	FooDB
Cichorium endivia	FooDB	FooDB
Cichorium intybus	FooDB	FooDB
Cinnamomum	FooDB	FooDB
Cinnamomum aromaticum	FooDB	FooDB
Cinnamomum verum	FooDB	FooDB
Cirsium	FooDB	FooDB
Citrullus lanatus	FooDB	FooDB
Citrus ×limon (L.) Burm. f. (pro sp.)	FooDB	FooDB
Citrus aurantiifolia	FooDB	FooDB
Citrus latifolia	FooDB	FooDB
Citrus limon	FooDB	FooDB
Citrus maxima	FooDB	FooDB
Citrus paradisi	FooDB	FooDB
Citrus reticulata	FooDB	FooDB
Citrus X sinensis (L.) Osbeck (pro. sp.)	FooDB	FooDB
Cocos nucifera	FooDB	FooDB
Coffea arabica L.	FooDB	FooDB
Coffea canephora	FooDB	FooDB
Colocasia esculenta	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Corchorus olitorius	FooDB	FooDB
Coriandrum sativum L.	FooDB	FooDB
Corylus	FooDB	FooDB
Corylus avellana	FooDB	FooDB
Crateva religiosa	FooDB	FooDB
Crocus sativus	FooDB	FooDB
Cucumis melo	FooDB	FooDB
Cucumis metuliferus	FooDB	FooDB
Cucumis sativus L.	FooDB	FooDB
Cucurbita	FooDB	FooDB
Cucurbita maxima	FooDB	FooDB
Cucurbita moschata	FooDB	FooDB
Cuminum cyminum	FooDB	FooDB
Curcuma longa	FooDB	FooDB
Cydonia oblonga	FooDB	FooDB
Cymbopogon citratus	FooDB	FooDB
Cynara cardunculus	FooDB	FooDB
Cynara scolymus	FooDB	FooDB
Daucus carota	FooDB	FooDB
Daucus carota ssp. sativus	FooDB	FooDB
Dimocarpus longan	FooDB	FooDB
Dioscorea	FooDB	FooDB
Dioscorea pentaphylla	FooDB	FooDB
Diospyros	FooDB	FooDB
Diospyros kaki	FooDB	FooDB
Diospyros virginiana	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Durio zibethinus	FooDB	FooDB
Dysphania ambrosioides	FooDB	FooDB
Elaeis	FooDB	FooDB
Eleocharis dulcis	FooDB	FooDB
Elettaria cardamomum	FooDB	FooDB
Empetrum nigrum	FooDB	FooDB
Equus caballus	FooDB	FooDB
Eragrostis tef	FooDB	FooDB
Eriobotrya japonica	FooDB	FooDB
Eruca vesicaria subsp. Sativa	FooDB	FooDB
Escherichia coli	Bacteria	KNApSAcK
Eugenia javanica	FooDB	FooDB
Eugenia uniflora	FooDB	FooDB
Eutrema japonicum	FooDB	FooDB
Fagopyrum esculentum	FooDB	FooDB
Fagopyrum tataricum	FooDB	FooDB
Fagus	FooDB	FooDB
Feijoa sellowiana	FooDB	FooDB
Ficus carica	FooDB	FooDB
Flammulina velutipes	FooDB	FooDB
Foeniculum vulgare	FooDB	FooDB
Fragaria x ananassa	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Garcinia mangostana	FooDB	FooDB
Gaylussacia baccata	FooDB	FooDB
Ginkgo biloba	FooDB	FooDB
Glycine max	FooDB	FooDB
Gossypium	FooDB	FooDB
Grifola frondosa	FooDB	FooDB
Hedysarum alpinum	FooDB	FooDB
Helianthus annuus L.	FooDB	FooDB
Helianthus tuberosus	FooDB	FooDB
Hibiscus sabbariffa	FooDB	FooDB
Hippophae rhamnoides	FooDB	FooDB
Hordeum vulgare	FooDB	FooDB
Hyssopus officinalis L.	FooDB	FooDB
Illicium verum	FooDB	FooDB
Ipomoea aquatica	FooDB	FooDB
Ipomoea batatas	FooDB	FooDB
Juglans	FooDB	FooDB
Juglans ailanthifolia	FooDB	FooDB
Juglans cinerea	FooDB	FooDB
Juglans nigra L.	FooDB	FooDB
Juglans regia	FooDB	FooDB
Lablab purpureus	FooDB	FooDB
Lactuca sativa	FooDB	FooDB
Lagenaria siceraria	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Lathyrus sativus	FooDB	FooDB
Laurus nobilis L.	FooDB	FooDB
Lens culinaris	FooDB	FooDB
Lentinus edodes	FooDB	FooDB
Lepidium sativum	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Levisticum officinale	FooDB	FooDB
Linum usitatissimum	FooDB	FooDB
Litchi chinensis	FooDB	FooDB
Luffa aegyptiaca	FooDB	FooDB
Lupinus	FooDB	FooDB
Lupinus albus	FooDB	FooDB
Macadamia	FooDB	FooDB
Macadamia tetraphylla	FooDB	FooDB
Malpighia emarginata	FooDB	FooDB
Malus	FooDB	FooDB
Malus pumila	FooDB	FooDB
Mammea americana	FooDB	FooDB
Mangifera indica	FooDB	FooDB
Manihot esculenta	FooDB	FooDB
Manilkara zapota	FooDB	FooDB
Maranta arundinacea	FooDB	FooDB
Matricaria recutita	FooDB	FooDB
Matteuccia struthiopteris	FooDB	FooDB
Medicago sativa	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Melissa officinalis L.	FooDB	FooDB
Mentha	FooDB	FooDB
Mentha aquatica	FooDB	FooDB
Mentha arvensis	FooDB	FooDB
Mentha spicata	FooDB	FooDB
Mentha x piperita	FooDB	FooDB
Mespilus germanica	FooDB	FooDB
Metroxylon sagu	FooDB	FooDB
Momordica charantia	FooDB	FooDB
Morchellaceae	FooDB	FooDB
Morella rubra	FooDB	FooDB
Moringa oleifera	FooDB	FooDB
Morus	FooDB	FooDB
Morus nigra	FooDB	FooDB
Mus musculus	LOTUS Database	35616633
Musa acuminata	FooDB	FooDB
Musa x paradisiaca	FooDB	FooDB
Myrica	FooDB	FooDB
Myristica fragrans	FooDB	FooDB
Nelumbo	FooDB	FooDB
Nelumbo nucifera	FooDB	FooDB
Nephelium lappaceum	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Nuphar lutea	FooDB	FooDB
Ocimum basilicum	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oenothera biennis	FooDB	FooDB
Olea europaea	FooDB	FooDB
Opuntia	FooDB	FooDB
Opuntia cochenillifera	FooDB	FooDB
Opuntia macrorhiza	FooDB	FooDB
Origanum majorana	FooDB	FooDB
Origanum onites	FooDB	FooDB
Origanum vulgare	FooDB	FooDB
Origanum X majoricum	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Oryza rufipogon	FooDB	FooDB
Oryza sativa	FooDB	FooDB
Ovis aries	FooDB	FooDB
Pachyrhizus erosus	FooDB	FooDB
Panax ginseng	FooDB	FooDB
Pangium edule	FooDB	FooDB
Panicum miliaceum	FooDB	FooDB
Passiflora edulis	FooDB	FooDB
Pastinaca sativa	FooDB	FooDB
Pediomelum esculentum	FooDB	FooDB
Perideridia oregana	FooDB	FooDB
Persea americana	FooDB	FooDB
Petasites japonicus	FooDB	FooDB
Petroselinum crispum	FooDB	FooDB
Phaseolus coccineus	FooDB	FooDB
Phaseolus lunatus	FooDB	FooDB
Phaseolus vulgaris	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Phoenix dactylifera	FooDB	FooDB
Photinia melanocarpa	FooDB	FooDB
Phyllostachys edulis	FooDB	FooDB
Physalis	FooDB	FooDB
Physalis philadelphica var. immaculata	FooDB	FooDB
Phytolacca americana	FooDB	FooDB
Pimenta dioica	FooDB	FooDB
Pimpinella anisum	FooDB	FooDB
Pinus	FooDB	FooDB
Pinus edulis	FooDB	FooDB
Piper nigrum L.	FooDB	FooDB
Pistacia vera	FooDB	FooDB
Pisum sativum	FooDB	FooDB
Pleurotus ostreatus	FooDB	FooDB
Polygonum alpinum	FooDB	FooDB
Portulaca oleracea	FooDB	FooDB
Pouteria sapota	FooDB	FooDB
Prunus armeniaca	FooDB	FooDB
Prunus avium	FooDB	FooDB
Prunus avium L.	FooDB	FooDB
Prunus cerasus	FooDB	FooDB
Prunus domestica	FooDB	FooDB
Prunus dulcis	FooDB	FooDB
Prunus persica	FooDB	FooDB
Prunus persica var. nucipersica	FooDB	FooDB
Prunus persica var. persica	FooDB	FooDB
Prunus tomentosa	FooDB	FooDB
Prunus virginiana	FooDB	FooDB
Psidium cattleianum	FooDB	FooDB
Psidium guajava	FooDB	FooDB
Psophocarpus tetragonolobus	FooDB	FooDB
Punica granatum	FooDB	FooDB
Pyrus communis	FooDB	FooDB
Pyrus pyrifolia	FooDB	FooDB
Quercus	FooDB	FooDB
Raphanus sativus	FooDB	FooDB
Raphanus sativus var. longipinnatus	FooDB	FooDB
Raphanus sativus var. sativus	FooDB	FooDB
Rheum rhabarbarum	FooDB	FooDB
Ribes aureum	FooDB	FooDB
Ribes glandulosum	FooDB	FooDB
Ribes nigrum	FooDB	FooDB
Ribes rubrum	FooDB	FooDB
Ribes uva-crispa	FooDB	FooDB
Rosa	FooDB	FooDB
Rubus arcticus	FooDB	FooDB
Rubus chamaemorus	FooDB	FooDB
Rubus idaeus	FooDB	FooDB
Rubus occidentalis	FooDB	FooDB
Rubus spectabilis	FooDB	FooDB
Rumex	FooDB	FooDB
Rumex acetosa	FooDB	FooDB
Rumex articus	FooDB	FooDB
Sagittaria latifolia	FooDB	FooDB
Salix pulchra	FooDB	FooDB
Salvia elegans	FooDB	FooDB
Salvia hispanica	FooDB	FooDB
Salvia officinalis	FooDB	FooDB
Salvia rosmarinus	FooDB	FooDB
Sambucus nigra	FooDB	FooDB
Sambucus nigra L.	FooDB	FooDB
Satureja hortensis L.	FooDB	FooDB
Satureja montana	FooDB	FooDB
Scorzonera hispanica	FooDB	FooDB
Secale cereale	FooDB	FooDB
Sechium edule	FooDB	FooDB
Sesamum indicum	FooDB	FooDB
Sesbania bispinosa	FooDB	FooDB
Sinapis alba	FooDB	FooDB
Sisymbrium	FooDB	FooDB
Solanum lycopersicum	FooDB	FooDB
Solanum lycopersicum var. cerasiforme	FooDB	FooDB
Solanum lycopersicum var. lycopersicum	FooDB	FooDB
Solanum melongena	FooDB	FooDB
Solanum quitoense	FooDB	FooDB
Solanum tuberosum	FooDB	FooDB
Sorbus aucuparia	FooDB	FooDB
Sorghum bicolor	FooDB	FooDB
Spinacia oleracea	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB
Syzygium aromaticum	FooDB	FooDB
Syzygium cumini	FooDB	FooDB
Syzygium jambos	FooDB	FooDB
Tamarindus indica	FooDB	FooDB
Taraxacum officinale	FooDB	FooDB
Tetragonia tetragonioides	FooDB	FooDB
Thelesperma	FooDB	FooDB
Thymus pulegioides	FooDB	FooDB
Thymus vulgaris	FooDB	FooDB
Tilia cordata	FooDB	FooDB
Tilia L.	FooDB	FooDB
Tragopogon porrifolius	FooDB	FooDB
Trigonella foenum-graecum	FooDB	FooDB
Triticum	FooDB	FooDB
Triticum aestivum	FooDB	FooDB
Triticum durum	FooDB	FooDB
Triticum spelta	FooDB	FooDB
Triticum turanicum	FooDB	FooDB
Trypanosoma brucei	LOTUS Database	35616633
Typha angustifolia	FooDB	FooDB
Vaccinium	FooDB	FooDB
Vaccinium angustifolium	FooDB	FooDB
Vaccinium angustifolium X Vaccinium corymbosum	FooDB	FooDB
Vaccinium arboreum	FooDB	FooDB
Vaccinium corymbosum	FooDB	FooDB
Vaccinium deliciosum	FooDB	FooDB
Vaccinium elliottii	FooDB	FooDB
Vaccinium macrocarpon	FooDB	FooDB
Vaccinium myrtilloides	FooDB	FooDB
Vaccinium myrtillus	FooDB	FooDB
Vaccinium ovalifolium	FooDB	FooDB
Vaccinium ovatum	FooDB	FooDB
Vaccinium oxycoccos	FooDB	FooDB
Vaccinium parvifolium	FooDB	FooDB
Vaccinium reticulatum	FooDB	FooDB
Vaccinium stamineum	FooDB	FooDB
Vaccinium uliginosum	FooDB	FooDB
Vaccinium vitis-idaea	FooDB	FooDB
Valerianella locusta	FooDB	FooDB
Vanilla	FooDB	FooDB
Verbena officinalis	FooDB	FooDB
Viburnum edule	FooDB	FooDB
Vicia faba	FooDB	FooDB
Vigna aconitifolia	FooDB	FooDB
Vigna angularis	FooDB	FooDB
Vigna mungo	FooDB	FooDB
Vigna radiata	FooDB	FooDB
Vigna umbellata	FooDB	FooDB
Vigna unguiculata	FooDB	FooDB
Vigna unguiculata ssp. cylindrica	FooDB	FooDB
Vigna unguiculata ssp. unguiculata	FooDB	FooDB
Vigna unguiculata var. sesquipedalis	FooDB	FooDB
Vitis	FooDB	FooDB
Vitis aestivalis	FooDB	FooDB
Vitis labrusca	FooDB	FooDB
Vitis rotundifolia	FooDB	FooDB
Vitis vinifera L.	FooDB	FooDB
Xanthosoma sagittifolium	FooDB	FooDB
Zea mays L.	FooDB	FooDB
Zingiber officinale	FooDB	FooDB
Zizania	FooDB	FooDB
Zizania aquatica	FooDB	FooDB
Ziziphus zizyphus	FooDB	FooDB

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

pyrimidine 2'-deoxyribonucleoside 5'-diphosphate (CHEBI:18075 )
thymidine phosphate (CHEBI:18075 )
Deoxyribonucleotides (C00363 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-0.87	ALOGPS
logP	-1.7	ChemAxon
logS	-1.8	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	77.16 m³·mol⁻¹	ChemAxon
Polarizability	32.12 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

External Links

HMDB ID

HMDB0001274

DrugBank ID

DB03103

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Thymidine_diphosphate

METLIN ID

6129

PubChem Compound

164628

PDB ID

Not Available

ChEBI ID

18075

Good Scents ID

Not Available

References

General References

Dahlmann N: Human serum thymidine triphosphate nucleotidohydrolase: purification and properties of a new enzyme. Biochemistry. 1982 Dec 21;21(26):6634-9. [PubMed:6297538 ]
Xu Y, Singh KV, Qin X, Murray BE, Weinstock GM: Analysis of a gene cluster of Enterococcus faecalis involved in polysaccharide biosynthesis. Infect Immun. 2000 Feb;68(2):815-23. doi: 10.1128/IAI.68.2.815-823.2000. [PubMed:10639451 ]
Vallon O: New sequence motifs in flavoproteins: evidence for common ancestry and tools to predict structure. Proteins. 2000 Jan 1;38(1):95-114. doi: 10.1002/(sici)1097-0134(20000101)38:1<95::aid-prot10>3.0.co;2-a. [PubMed:10651042 ]
Sheu SJ, Wu SN: Mechanism of inhibitory actions of oxidizing agents on calcium-activated potassium current in cultured pigment epithelial cells of the human retina. Invest Ophthalmol Vis Sci. 2003 Mar;44(3):1237-44. doi: 10.1167/iovs.02-0330. [PubMed:12601054 ]
Costantini P, Belzacq AS, Vieira HL, Larochette N, de Pablo MA, Zamzami N, Susin SA, Brenner C, Kroemer G: Oxidation of a critical thiol residue of the adenine nucleotide translocator enforces Bcl-2-independent permeability transition pore opening and apoptosis. Oncogene. 2000 Jan 13;19(2):307-14. doi: 10.1038/sj.onc.1203299. [PubMed:10645010 ]

Showing NP-Card for dTDP (NP0044268)

MOL for NP0044268 (dTDP)

3D MOL for NP0044268 (dTDP)

3D SDF for NP0044268 (dTDP)

3D-SDF for NP0044268 (dTDP)

PDB for NP0044268 (dTDP)

3D PDB for NP0044268 (dTDP)

SMILES for NP0044268 (dTDP)

INCHI for NP0044268 (dTDP)

Structure for NP0044268 (dTDP)

3D Structure for NP0044268 (dTDP)