NP-MRD: Showing NP-Card for Uridine 5'-diphosphate (NP0001022)

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Record Information

Version

1.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2021-07-01 14:27:35 UTC

NP-MRD ID

NP0001022

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Uridine 5'-diphosphate

Description

Uridine 5'-diphosphate, also known as 5'-UDP, UDP or uridine diphosphoric acid, belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. UDP is also classified as a nucleotide diphosphate. It is an ester of pyrophosphoric acid with the nucleoside uridine. UDP consists of a pyrophosphate group, a pentose sugar ribose, and the nucleobase uracil. UDP exists in all living species, ranging from bacteria to plants to humans. In mammals UDP is an important factor in glycogenesis or the formation of glycogen in the liver. Before glucose can be stored as glycogen in the liver and muscles, the enzyme UDP-glucose pyrophosphorylase forms a UDP-glucose unit by combining glucose 1-phosphate with uridine triphosphate, cleaving a pyrophosphate ion in the process. Then, the enzyme glycogen synthase combines UDP-glucose units to form a glycogen chain. UDP is also an important extracellular pyrimidine signaling molecule that mediates diverse biological effects via P1 and P2 purinergic receptors, such as the uptake of thymidine and proliferation of gliomas. UDP plays a key role in the function of Uridine 5'-diphospho-glucuronosyltransferases (UDP-glucuronosyltransferases, UGTs) which catalyze the transfer of the glucuronic acid component of UDP-glucuronic acid to a small hydrophobic molecule. UDP-Glucuronosyltransferases are responsible for the process of glucuronidation, a major part of phase II metabolism. The reaction catalyzed by UGT enzymes involves the addition of a glucuronic acid moiety to xenobiotics and is the most important pathway for the human body's elimination of the most frequently prescribed drugs. It is also the major pathway for foreign chemical (dietary, environmental, pharmaceutical) removal for most drugs, dietary substances, toxins and endogenous substances. UGT is present in humans, other animals, plants, and bacteria. Famously, UGT enzymes are not present in the genus Felis (PMID: 10862526 ) And this accounts for a number of unusual toxicities in the cat family.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0000295
     RDKit          3D
Uridine 5'-diphosphate
 39 40  0  0  0  0  0  0  0  0999 V2000
   -4.9570    3.8585   -1.5266 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2798    2.9152   -1.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9279    3.1104   -0.7726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2244    2.0628   -0.2429 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8031    0.8749    0.0193 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0639   -0.2390    0.5804 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7237    0.1381    0.6310 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0191   -1.0694    0.6414 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4193   -0.7402    0.3197 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2255   -1.8724    0.3004 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8200   -1.4474   -0.0635 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.5360   -1.2553    1.2614 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4977   -2.7471   -0.9180 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9175   -0.0935   -1.0368 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9543    1.0835   -0.4588 P   0  0  0  0  0  5  0  0  0  0  0  0
    6.3751    0.6885   -0.8604 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6253    2.5445   -1.2309 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9397    1.2243    1.2099 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6822   -1.9298   -0.3760 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6369   -3.2777   -0.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1360   -1.4739   -0.2870 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8659   -2.4279    0.4267 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1142    0.6970   -0.2427 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7137   -0.3874   -0.0209 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7976    1.7187   -0.7587 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4652    4.0831   -0.9900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1749    2.1595   -0.0176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3684   -0.4403    1.6338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1376   -1.5010    1.6447 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7716   -0.0479    1.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5159   -0.2196   -0.6513 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1443   -3.6033   -0.6135 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3438    3.2557   -0.5799 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1885    1.8178    1.4545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3050   -1.7677   -1.4056 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2453   -3.6766   -0.1343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5515   -1.2829   -1.2792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7560   -2.3127    1.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8158    1.5803   -0.9620 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
  8 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
  5 23  1  0
 23 24  2  0
 23 25  1  0
 25  2  1  0
 21  6  1  0
  3 26  1  0
  4 27  1  0
  6 28  1  1
  8 29  1  1
  9 30  1  0
  9 31  1  0
 13 32  1  0
 17 33  1  0
 18 34  1  0
 19 35  1  6
 20 36  1  0
 21 37  1  6
 22 38  1  0
 25 39  1  0
M  END


  Mrv1652306262018212D          

 25 26  0  0  0  0            999 V2000
 9998.433210001.5481    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.222310001.5399    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.6882 9999.6899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.211410000.9255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.403510000.1010    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.1168 9999.6899    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9995.7809 9998.4518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.832110000.1010    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.7066 9998.9756    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.5312 9998.9756    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.5536 9999.7023    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10003.1414 9998.9880    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10004.269010000.1133    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.9659 9998.9880    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.210010000.1022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4955 9999.6897    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4955 9998.8646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2100 9998.4522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.9245 9998.8646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.9245 9999.6897    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3096 9999.6069    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.642210000.0919    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.897110000.8765    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.722110000.8765    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.977010000.0919    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
  6 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 20  1  0  0  0  0
 19 20  1  0  0  0  0
 15  4  2  0  0  0  0
 17  7  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 21 22  1  0  0  0  0
 21 25  1  0  0  0  0
 23  1  1  6  0  0  0
 22 20  1  1  0  0  0
 24  2  1  6  0  0  0
 25  3  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0001022

> <DATABASE_NAME>
NP-MRD

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

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

> <INCHI_KEY>
XCCTYIAWTASOJW-XVFCMESISA-N

> <FORMULA>
C9H14N2O12P2

> <MOLECULAR_WEIGHT>
404.1612

> <EXACT_MASS>
404.002196946

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
30.434393627025816

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.94

> <JCHEM_LOGP>
-2.960606651999999

> <ALOGPS_LOGS>
-1.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.210398156718922

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7717429601440289

> <JCHEM_PKA_STRONGEST_BASIC>
-3.664543362840705

> <JCHEM_POLAR_SURFACE_AREA>
212.38999999999996

> <JCHEM_REFRACTIVITY>
74.31139999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.89e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
UDP

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000295
     RDKit          3D
Uridine 5'-diphosphate
 39 40  0  0  0  0  0  0  0  0999 V2000
   -4.9570    3.8585   -1.5266 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2798    2.9152   -1.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9279    3.1104   -0.7726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2244    2.0628   -0.2429 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8031    0.8749    0.0193 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0639   -0.2390    0.5804 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7237    0.1381    0.6310 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0191   -1.0694    0.6414 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4193   -0.7402    0.3197 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2255   -1.8724    0.3004 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8200   -1.4474   -0.0635 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.5360   -1.2553    1.2614 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4977   -2.7471   -0.9180 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9175   -0.0935   -1.0368 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9543    1.0835   -0.4588 P   0  0  0  0  0  5  0  0  0  0  0  0
    6.3751    0.6885   -0.8604 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6253    2.5445   -1.2309 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9397    1.2243    1.2099 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6822   -1.9298   -0.3760 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6369   -3.2777   -0.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1360   -1.4739   -0.2870 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8659   -2.4279    0.4267 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1142    0.6970   -0.2427 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7137   -0.3874   -0.0209 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7976    1.7187   -0.7587 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4652    4.0831   -0.9900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1749    2.1595   -0.0176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3684   -0.4403    1.6338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1376   -1.5010    1.6447 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7716   -0.0479    1.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5159   -0.2196   -0.6513 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1443   -3.6033   -0.6135 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3438    3.2557   -0.5799 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1885    1.8178    1.4545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3050   -1.7677   -1.4056 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2453   -3.6766   -0.1343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5515   -1.2829   -1.2792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7560   -2.3127    1.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8158    1.5803   -0.9620 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
  8 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
  5 23  1  0
 23 24  2  0
 23 25  1  0
 25  2  1  0
 21  6  1  0
  3 26  1  0
  4 27  1  0
  6 28  1  1
  8 29  1  1
  9 30  1  0
  9 31  1  0
 13 32  1  0
 17 33  1  0
 18 34  1  0
 19 35  1  6
 20 36  1  0
 21 37  1  6
 22 38  1  0
 25 39  1  0
M  END

HEADER    PROTEIN                                 26-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-JUN-20         0                                  
HETATM    1  O   UNK     0    8663.7428669.556   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8667.0828669.541   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8667.9518666.088   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8661.4618668.394   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8669.2878666.855   0.000  0.00  0.00           O+0
HETATM    6  P   UNK     0    8670.6188666.088   0.000  0.00  0.00           P+0
HETATM    7  O   UNK     0    8658.7918663.777   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0    8671.9538666.855   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8669.8528664.754   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8671.3928664.754   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0    8673.3008666.111   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0    8672.5318664.778   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8674.6358666.878   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0    8674.0708664.778   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0    8661.4598666.857   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0    8660.1258666.087   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0    8660.1258664.547   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8661.4598663.777   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8662.7928664.547   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0    8662.7928666.087   0.000  0.00  0.00           N+0
HETATM   21  O   UNK     0    8665.3788665.933   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0    8664.1328666.838   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8664.6088668.303   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0    8666.1488668.303   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0    8666.6248666.838   0.000  0.00  0.00           C+0
CONECT    1   23                                                            
CONECT    2   24                                                            
CONECT    3    5   25                                                       
CONECT    4   15                                                            
CONECT    5    3    6                                                       
CONECT    6    5    8    9   10                                             
CONECT    7   17                                                            
CONECT    8    6   11                                                       
CONECT    9    6                                                            
CONECT   10    6                                                            
CONECT   11    8   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
CONECT   15   16   20    4                                                  
CONECT   16   15   17                                                       
CONECT   17   18   16    7                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   15   19   22                                                  
CONECT   21   22   25                                                       
CONECT   22   23   21   20                                                  
CONECT   23   22   24    1                                                  
CONECT   24   23   25    2                                                  
CONECT   25   24   21    3                                                  
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

COMPND    HMDB0000295
HETATM    1  O1  UNL     1      -4.957   3.859  -1.527  1.00  0.00           O  
HETATM    2  C1  UNL     1      -4.280   2.915  -1.039  1.00  0.00           C  
HETATM    3  C2  UNL     1      -2.928   3.110  -0.773  1.00  0.00           C  
HETATM    4  C3  UNL     1      -2.224   2.063  -0.243  1.00  0.00           C  
HETATM    5  N1  UNL     1      -2.803   0.875   0.019  1.00  0.00           N  
HETATM    6  C4  UNL     1      -2.064  -0.239   0.580  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.724   0.138   0.631  1.00  0.00           O  
HETATM    8  C5  UNL     1      -0.019  -1.069   0.641  1.00  0.00           C  
HETATM    9  C6  UNL     1       1.419  -0.740   0.320  1.00  0.00           C  
HETATM   10  O3  UNL     1       2.226  -1.872   0.300  1.00  0.00           O  
HETATM   11  P1  UNL     1       3.820  -1.447  -0.064  1.00  0.00           P  
HETATM   12  O4  UNL     1       4.536  -1.255   1.261  1.00  0.00           O  
HETATM   13  O5  UNL     1       4.498  -2.747  -0.918  1.00  0.00           O  
HETATM   14  O6  UNL     1       3.917  -0.094  -1.037  1.00  0.00           O  
HETATM   15  P2  UNL     1       4.954   1.084  -0.459  1.00  0.00           P  
HETATM   16  O7  UNL     1       6.375   0.689  -0.860  1.00  0.00           O  
HETATM   17  O8  UNL     1       4.625   2.544  -1.231  1.00  0.00           O  
HETATM   18  O9  UNL     1       4.940   1.224   1.210  1.00  0.00           O  
HETATM   19  C7  UNL     1      -0.682  -1.930  -0.376  1.00  0.00           C  
HETATM   20  O10 UNL     1      -0.637  -3.278  -0.107  1.00  0.00           O  
HETATM   21  C8  UNL     1      -2.136  -1.474  -0.287  1.00  0.00           C  
HETATM   22  O11 UNL     1      -2.866  -2.428   0.427  1.00  0.00           O  
HETATM   23  C9  UNL     1      -4.114   0.697  -0.243  1.00  0.00           C  
HETATM   24  O12 UNL     1      -4.714  -0.387  -0.021  1.00  0.00           O  
HETATM   25  N2  UNL     1      -4.798   1.719  -0.759  1.00  0.00           N  
HETATM   26  H1  UNL     1      -2.465   4.083  -0.990  1.00  0.00           H  
HETATM   27  H2  UNL     1      -1.175   2.159  -0.018  1.00  0.00           H  
HETATM   28  H3  UNL     1      -2.368  -0.440   1.634  1.00  0.00           H  
HETATM   29  H4  UNL     1      -0.138  -1.501   1.645  1.00  0.00           H  
HETATM   30  H5  UNL     1       1.772  -0.048   1.103  1.00  0.00           H  
HETATM   31  H6  UNL     1       1.516  -0.220  -0.651  1.00  0.00           H  
HETATM   32  H7  UNL     1       4.144  -3.603  -0.613  1.00  0.00           H  
HETATM   33  H8  UNL     1       4.344   3.256  -0.580  1.00  0.00           H  
HETATM   34  H9  UNL     1       4.189   1.818   1.455  1.00  0.00           H  
HETATM   35  H10 UNL     1      -0.305  -1.768  -1.406  1.00  0.00           H  
HETATM   36  H11 UNL     1       0.245  -3.677  -0.134  1.00  0.00           H  
HETATM   37  H12 UNL     1      -2.551  -1.283  -1.279  1.00  0.00           H  
HETATM   38  H13 UNL     1      -2.756  -2.313   1.404  1.00  0.00           H  
HETATM   39  H14 UNL     1      -5.816   1.580  -0.962  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   25
CONECT    3    4    4   26
CONECT    4    5   27
CONECT    5    6   23
CONECT    6    7   21   28
CONECT    7    8
CONECT    8    9   19   29
CONECT    9   10   30   31
CONECT   10   11
CONECT   11   12   12   13   14
CONECT   13   32
CONECT   14   15
CONECT   15   16   16   17   18
CONECT   17   33
CONECT   18   34
CONECT   19   20   21   35
CONECT   20   36
CONECT   21   22   37
CONECT   22   38
CONECT   23   24   24   25
CONECT   25   39
END

HMDB0000295
     RDKit          3D
Uridine 5'-diphosphate
 39 40  0  0  0  0  0  0  0  0999 V2000
   -4.9570    3.8585   -1.5266 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2798    2.9152   -1.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9279    3.1104   -0.7726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2244    2.0628   -0.2429 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8031    0.8749    0.0193 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0639   -0.2390    0.5804 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7237    0.1381    0.6310 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0191   -1.0694    0.6414 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4193   -0.7402    0.3197 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2255   -1.8724    0.3004 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8200   -1.4474   -0.0635 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.5360   -1.2553    1.2614 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4977   -2.7471   -0.9180 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9175   -0.0935   -1.0368 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9543    1.0835   -0.4588 P   0  0  0  0  0  5  0  0  0  0  0  0
    6.3751    0.6885   -0.8604 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6253    2.5445   -1.2309 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9397    1.2243    1.2099 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6822   -1.9298   -0.3760 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6369   -3.2777   -0.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1360   -1.4739   -0.2870 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8659   -2.4279    0.4267 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1142    0.6970   -0.2427 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7137   -0.3874   -0.0209 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7976    1.7187   -0.7587 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4652    4.0831   -0.9900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1749    2.1595   -0.0176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3684   -0.4403    1.6338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1376   -1.5010    1.6447 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7716   -0.0479    1.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5159   -0.2196   -0.6513 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1443   -3.6033   -0.6135 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3438    3.2557   -0.5799 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1885    1.8178    1.4545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3050   -1.7677   -1.4056 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2453   -3.6766   -0.1343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5515   -1.2829   -1.2792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7560   -2.3127    1.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8158    1.5803   -0.9620 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
  8 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
  5 23  1  0
 23 24  2  0
 23 25  1  0
 25  2  1  0
 21  6  1  0
  3 26  1  0
  4 27  1  0
  6 28  1  1
  8 29  1  1
  9 30  1  0
  9 31  1  0
 13 32  1  0
 17 33  1  0
 18 34  1  0
 19 35  1  6
 20 36  1  0
 21 37  1  6
 22 38  1  0
 25 39  1  0
M  END

View in JSmol

Synonyms

Value	Source
Uridine diphosphate	ChEBI
Uridine diphosphoric acid	Generator
Uridine 5'-diphosphoric acid	Generator
5'-UDP	HMDB
UDP	HMDB
Uridine 5'-pyrophosphate	HMDB
Uridine 5'-pyrophosphorate	HMDB
Uridine 5'-pyrophosphoric acid	HMDB
Uridine pyrophosphate	HMDB
Pyrophosphate, uridine	HMDB
Diphosphate, uridine	HMDB
5’-UDP	HMDB
Uridine 5'-(trihydrogen pyrophosphate)	HMDB
Uridine 5’-(trihydrogen pyrophosphate)	HMDB
Uridine 5’-diphosphate	HMDB
Uridine 5’-diphosphoric acid	HMDB
Uridine 5’-pyrophosphate	HMDB
Uridine 5’-pyrophosphoric acid	HMDB
Uridine 5'-diphosphate	HMDB

Chemical Formula

C₉H₁₄N₂O₁₂P₂

Average Mass

404.1612 Da

Monoisotopic Mass

404.00220 Da

IUPAC Name

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

Traditional Name

UDP

CAS Registry Number

58-98-0

SMILES

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

InChI Identifier

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

InChI Key

XCCTYIAWTASOJW-XVFCMESISA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

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
Arabidopsis thaliana	KNApSAcK Database	22123792
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
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
Paraburkholderia phymatum	-	KNApSAcK
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
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	Dr. Duke's Phytochemical and Ethnobotanical Databases
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

Species Where Detected

Species Name	Source	Reference
Escherichia coli	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate 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 diphosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside diphosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Organic pyrophosphate
Hydroxypyrimidine
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Alcohol
Organopnictogen compound
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine ribonucleoside 5'-diphosphate (CHEBI:17659 )
uridine 5'-phosphate (CHEBI:17659 )
Ribonucleotides (C00015 )

Physical Properties

State

Solid

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
Water Solubility	8.89 g/L	ALOGPS
logP	-0.94	ALOGPS
logP	-3	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	212.39 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	74.31 m³·mol⁻¹	ChemAxon
Polarizability	30.43 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

External Links

HMDB ID

HMDB0000295

DrugBank ID

DB03435

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

Not Available

PubChem Compound

6031

PDB ID

Not Available

ChEBI ID

17659

Good Scents ID

Not Available

References

General References

Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
Brouwer A, Morse DC, Lans MC, Schuur AG, Murk AJ, Klasson-Wehler E, Bergman A, Visser TJ: Interactions of persistent environmental organohalogens with the thyroid hormone system: mechanisms and possible consequences for animal and human health. Toxicol Ind Health. 1998 Jan-Apr;14(1-2):59-84. [PubMed:9460170 ]
Kamisako T, Kobayashi Y, Takeuchi K, Ishihara T, Higuchi K, Tanaka Y, Gabazza EC, Adachi Y: Recent advances in bilirubin metabolism research: the molecular mechanism of hepatocyte bilirubin transport and its clinical relevance. J Gastroenterol. 2000;35(9):659-64. [PubMed:11023036 ]
Syme MR, Paxton JW, Keelan JA: Drug transfer and metabolism by the human placenta. Clin Pharmacokinet. 2004;43(8):487-514. [PubMed:15170365 ]
Collier AC, Tingle MD, Paxton JW, Mitchell MD, Keelan JA: Metabolizing enzyme localization and activities in the first trimester human placenta: the effect of maternal and gestational age, smoking and alcohol consumption. Hum Reprod. 2002 Oct;17(10):2564-72. [PubMed:12351530 ]
Morrone FB, Jacques-Silva MC, Horn AP, Bernardi A, Schwartsmann G, Rodnight R, Lenz G: Extracellular nucleotides and nucleosides induce proliferation and increase nucleoside transport in human glioma cell lines. J Neurooncol. 2003 Sep;64(3):211-8. [PubMed:14558596 ]
Rise A: [Drugs and the fetus]. Tidsskr Nor Laegeforen. 1976 Jan 10;96(1):41-2. [PubMed:1257952 ]
Court MH, Greenblatt DJ: Molecular genetic basis for deficient acetaminophen glucuronidation by cats: UGT1A6 is a pseudogene, and evidence for reduced diversity of expressed hepatic UGT1A isoforms. Pharmacogenetics. 2000 Jun;10(4):355-69. doi: 10.1097/00008571-200006000-00009. [PubMed:10862526 ]

Showing NP-Card for Uridine 5'-diphosphate (NP0001022)

MOL for NP0001022 (Uridine 5'-diphosphate)

3D MOL for NP0001022 (Uridine 5'-diphosphate)

3D SDF for NP0001022 (Uridine 5'-diphosphate)

3D-SDF for NP0001022 (Uridine 5'-diphosphate)

PDB for NP0001022 (Uridine 5'-diphosphate)

3D PDB for NP0001022 (Uridine 5'-diphosphate)

SMILES for NP0001022 (Uridine 5'-diphosphate)

INCHI for NP0001022 (Uridine 5'-diphosphate)

Structure for NP0001022 (Uridine 5'-diphosphate)

3D Structure for NP0001022 (Uridine 5'-diphosphate)