NP-MRD: Showing NP-Card for {[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid (NP0314616)

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Record Information

Version

1.0

Created at

2022-09-11 12:48:08 UTC

Updated at

2022-09-11 12:48:08 UTC

NP-MRD ID

NP0314616

Secondary Accession Numbers

None

Natural Product Identification

Common Name

{[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid

Description

UDP - Na belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. {[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid is found in Helianthus tuberosus. UDP - Na is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652310061716262D          

 25 26  0  0  0  0            999 V2000
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2871    2.6392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9225    1.6607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3086    2.0038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4143   -0.0143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9044    1.5549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3748    0.5154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9440    1.0253    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1155    1.8322    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.1594    0.7703    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
 10  5  2  0  0  0  0
 10  9  1  0  0  0  0
 11  2  1  0  0  0  0
 11  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  5  1  0  0  0  0
 13  6  1  0  0  0  0
 14  7  1  0  0  0  0
 15  9  2  0  0  0  0
 21  3  1  0  0  0  0
 22  4  1  0  0  0  0
 22  8  1  0  0  0  0
 24 16  1  0  0  0  0
 24 17  1  0  0  0  0
 24 18  2  0  0  0  0
 24 23  1  0  0  0  0
 25 19  1  0  0  0  0
 25 20  2  0  0  0  0
 25 21  1  0  0  0  0
 25 23  1  0  0  0  0
M  END

     RDKit          3D

 39 40  0  0  0  0  0  0  0  0999 V2000
   -3.1499    1.0604    2.4996 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7480    0.3768    1.6064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0394    0.2045    1.7658 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7753   -0.5059    0.8466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1340   -0.6757    1.0209 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0968   -1.0125   -0.2254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7246   -0.8176   -0.3560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0257   -0.1127    0.5736 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6195    0.1105    0.5394 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0111   -0.4505   -0.6271 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2281    0.0223   -0.5225 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3675   -0.3044   -1.3867 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8208   -1.6312   -1.1862 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3086   -1.5205   -0.3991 P   0  0  2  0  0  5  0  0  0  0  0  0
    3.4445   -2.7521    0.4632 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1746   -0.2112    0.7421 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6609   -1.1800   -1.2963 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8953   -0.6631   -0.2238 P   0  0  0  0  0  5  0  0  0  0  0  0
    7.0924   -0.2978   -1.0274 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3651    0.6404    0.6989 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3185   -1.9073    0.8459 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1077    1.5124   -0.2937 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0682    2.1864   -1.4606 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1844    1.5324    0.5222 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8044    1.9645    1.8156 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5772   -0.2593    1.8307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6168   -1.5634   -0.9861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1836   -1.1711   -1.2029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1099   -0.3990    1.4180 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5366   -0.4110    0.5729 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1042    0.4356   -1.5192 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8890   -0.4256   -2.4675 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1055    0.6340    0.2024 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6323    1.5068    0.3459 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5231   -2.2186    1.3020 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9807    1.8836    0.3090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4787    3.0140   -1.3433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9101    2.2162    0.0752 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4340    1.1894    2.3119 H   0  0  0  0  0  0  0  0  0  0  0  0
 23 22  1  0
 22 11  1  0
 11 12  1  0
 12 13  1  0
 14 13  1  6
 14 16  1  0
 14 15  2  0
 14 17  1  0
 17 18  1  0
 18 20  1  0
 18 21  1  0
 18 19  2  0
 11 10  1  0
 10  9  1  0
  9 24  1  0
 24 25  1  0
  9  8  1  0
  8  7  1  0
  7  6  2  0
  6  4  1  0
  4  5  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
 24 22  1  0
  2  8  1  0
 23 37  1  0
 22 36  1  1
 11 30  1  1
 12 31  1  0
 12 32  1  0
 16 33  1  0
 20 34  1  0
 21 35  1  0
  9 29  1  1
 24 38  1  6
 25 39  1  0
  7 28  1  0
  6 27  1  0
  5 26  1  0
M  END


  Mrv1652310061716262D          

 25 26  0  0  0  0            999 V2000
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2871    2.6392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9225    1.6607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3086    2.0038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4143   -0.0143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9044    1.5549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3748    0.5154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9440    1.0253    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1155    1.8322    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.1594    0.7703    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
 10  5  2  0  0  0  0
 10  9  1  0  0  0  0
 11  2  1  0  0  0  0
 11  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  5  1  0  0  0  0
 13  6  1  0  0  0  0
 14  7  1  0  0  0  0
 15  9  2  0  0  0  0
 21  3  1  0  0  0  0
 22  4  1  0  0  0  0
 22  8  1  0  0  0  0
 24 16  1  0  0  0  0
 24 17  1  0  0  0  0
 24 18  2  0  0  0  0
 24 23  1  0  0  0  0
 25 19  1  0  0  0  0
 25 20  2  0  0  0  0
 25 21  1  0  0  0  0
 25 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0314616

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1C(COP(O)(=O)OP(O)(O)=O)OC(C1O)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)

> <INCHI_KEY>
XCCTYIAWTASOJW-UHFFFAOYSA-N

> <FORMULA>
C9H14N2O12P2

> <MOLECULAR_WEIGHT>
404.161

> <EXACT_MASS>
404.002197895

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
31.01071354369603

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.18

> <JCHEM_LOGP>
-2.960606651999999

> <ALOGPS_LOGS>
-1.58

> <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>
212.39

> <JCHEM_REFRACTIVITY>
74.31139999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.07e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
uridine diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-OCT-17         0                                  
HETATM    1  C   UNK     0       3.182  -6.383   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.087  -5.138   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.846  -0.544   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.381  -1.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.650  -6.222   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.366  -2.485   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.929  -3.570   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       1.024  -4.816   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       3.460  -3.731   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       0.745  -7.468   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       5.136   1.425   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       2.425  -0.544   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.302  -2.163   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      11.736   4.927   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      12.922   3.100   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       9.909   3.740   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      10.107  -0.027   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.155   2.903   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       8.166   0.962   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       5.906  -2.485   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      11.095   1.914   0.000  0.00  0.00           O+0
HETATM   24  P   UNK     0      11.416   3.420   0.000  0.00  0.00           P+0
HETATM   25  P   UNK     0       9.631   1.438   0.000  0.00  0.00           P+0
CONECT    1    2    5                                                       
CONECT    2    1   11                                                       
CONECT    3    4   21                                                       
CONECT    4    3    6   22                                                  
CONECT    5    1   10   12                                                  
CONECT    6    4    7   13                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7   11   22                                                  
CONECT    9   10   11   15                                                  
CONECT   10    5    9                                                       
CONECT   11    2    8    9                                                  
CONECT   12    5                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    9                                                            
CONECT   16   24                                                            
CONECT   17   24                                                            
CONECT   18   24                                                            
CONECT   19   25                                                            
CONECT   20   25                                                            
CONECT   21    3   25                                                       
CONECT   22    4    8                                                       
CONECT   23   24   25                                                       
CONECT   24   16   17   18   23                                             
CONECT   25   19   20   21   23                                             
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₁₄N₂O₁₂P₂

Average Mass

404.1610 Da

Monoisotopic Mass

404.00220 Da

IUPAC Name

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

Traditional Name

uridine diphosphate

CAS Registry Number

Not Available

SMILES

OC1C(COP(O)(=O)OP(O)(O)=O)OC(C1O)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)

InChI Key

XCCTYIAWTASOJW-UHFFFAOYSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Helianthus tuberosus	LOTUS Database	35616633

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
Pentose monosaccharide
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Vinylogous amide
Heteroaromatic compound
Tetrahydrofuran
1,2-diol
Urea
Secondary alcohol
Lactam
Azacycle
Oxacycle
Organoheterocyclic compound
Organic oxygen compound
Alcohol
Organopnictogen compound
Organic oxide
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

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	-1.2	ALOGPS
logP	-3	ChemAxon
logS	-1.6	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	31.01 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

HMDB0156308

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

1158

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for {[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid (NP0314616)

MOL for NP0314616 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid)

3D MOL for NP0314616 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid)

3D SDF for NP0314616 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid)

3D-SDF for NP0314616 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid)

PDB for NP0314616 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid)

3D PDB for NP0314616 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid)

SMILES for NP0314616 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid)

INCHI for NP0314616 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid)

Structure for NP0314616 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid)

3D Structure for NP0314616 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid)