NP-MRD: Showing NP-Card for [hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid (NP0218291)

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Record Information

Version

1.0

Created at

2022-09-05 18:54:33 UTC

Updated at

2022-09-05 18:54:33 UTC

NP-MRD ID

NP0218291

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid

Description

DTDP-4-dehydro-2,3,6-trideoxy-alpha-D-glucose, also known as dTDP-4-oxo-2,3,6-trideoxy-D-glucose or dTDP-4-dehydro-2,3,6-trideoxy-α-D-hexopyranose, belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group. DTDP-4-dehydro-2,3,6-trideoxy-alpha-D-glucose is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. [hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid is found in Apis cerana. It was first documented in 2008 (PMID: 18345667). Based on a literature review very few articles have been published on dTDP-4-dehydro-2,3,6-trideoxy-alpha-D-glucose (PMID: 26612347).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309052220542D          

 33 35  0  0  1  0            999 V2000
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5253   -5.4349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2704   -6.2195    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7553   -6.8870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4454   -6.2195    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9605   -6.8870    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2960   -7.6407    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8111   -8.3081    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.4785   -8.7930    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1437   -7.8232    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3262   -8.9755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6617   -9.7292    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.4154   -9.3937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9081  -10.0648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9973  -10.4829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5124  -11.1503    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8479  -11.9040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3630  -12.5714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5425  -12.4852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0576  -13.1526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2070  -11.7315    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6135  -11.6453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6919  -11.0641    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904   -5.4349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 16 19  1  0  0  0  0
 20 19  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
 20 27  1  0  0  0  0
  9 28  1  0  0  0  0
  5 28  1  0  0  0  0
  4 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
  2 32  1  0  0  0  0
 32 33  1  0  0  0  0
M  END


  Mrv1652309052220542D          

 33 35  0  0  1  0            999 V2000
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5253   -5.4349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2704   -6.2195    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7553   -6.8870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4454   -6.2195    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9605   -6.8870    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2960   -7.6407    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8111   -8.3081    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.4785   -8.7930    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1437   -7.8232    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3262   -8.9755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6617   -9.7292    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.4154   -9.3937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9081  -10.0648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9973  -10.4829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5124  -11.1503    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8479  -11.9040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3630  -12.5714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5425  -12.4852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0576  -13.1526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2070  -11.7315    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6135  -11.6453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6919  -11.0641    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904   -5.4349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 16 19  1  0  0  0  0
 20 19  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
 20 27  1  0  0  0  0
  9 28  1  0  0  0  0
  5 28  1  0  0  0  0
  4 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
  2 32  1  0  0  0  0
 32 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0218291

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1O[C@@H](CCC1=O)OP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)N1C=C(C)C(O)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H24N2O13P2/c1-8-6-18(16(22)17-15(8)21)13-5-11(20)12(29-13)7-27-32(23,24)31-33(25,26)30-14-4-3-10(19)9(2)28-14/h6,9,11-14,20H,3-5,7H2,1-2H3,(H,23,24)(H,25,26)(H,17,21,22)/t9-,11+,12-,13-,14-/m1/s1

> <INCHI_KEY>
YINKRXMSCURQIS-RHZHCTOVSA-N

> <FORMULA>
C16H24N2O13P2

> <MOLECULAR_WEIGHT>
514.317

> <EXACT_MASS>
514.075362837

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
57

> <JCHEM_AVERAGE_POLARIZABILITY>
43.52017028784593

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[hydroxy({[(2R,6R)-6-methyl-5-oxooxan-2-yl]oxy})phosphoryl]oxy}({[(2R,3S,5R)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinic acid

> <JCHEM_LOGP>
-0.2653794393333333

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1837837408425087

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7445690791521908

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2403568921139057

> <JCHEM_POLAR_SURFACE_AREA>
210.94999999999996

> <JCHEM_REFRACTIVITY>
104.87819999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[hydroxy([(2R,6R)-6-methyl-5-oxooxan-2-yl]oxy)phosphoryl]oxy([(2R,3S,5R)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       5.335  -7.700   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.581 -10.145   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.105 -11.610   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       7.010 -12.856   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.565 -11.610   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.660 -12.856   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.286 -14.263   0.000  0.00  0.00           O+0
HETATM   12  P   UNK     0       3.381 -15.508   0.000  0.00  0.00           P+0
HETATM   13  O   UNK     0       4.627 -16.414   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       2.135 -14.603   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.476 -16.754   0.000  0.00  0.00           O+0
HETATM   16  P   UNK     0       3.102 -18.161   0.000  0.00  0.00           P+0
HETATM   17  O   UNK     0       4.509 -17.535   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.695 -18.788   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       3.728 -19.568   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.823 -20.814   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.449 -22.221   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.544 -23.467   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.013 -23.306   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       0.108 -24.552   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       0.386 -21.899   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.145 -21.738   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       1.292 -20.653   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       4.089 -10.145   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   31  N   UNK     0       4.001  -5.390   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   32                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   29                                                  
CONECT    5    4    6   28                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   28                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   12   16                                                       
CONECT   16   15   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16   20                                                       
CONECT   20   19   21   27                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   20                                                       
CONECT   28    9    5                                                       
CONECT   29    4   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31    2   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

View in JSmol

Synonyms

Value	Source
dTDP-4-oxo-2,3,6-Trideoxy-D-glucose	ChEBI
dTDP-[(2R,6R)-Tetrahydro-6-methyl-5-oxo-2H-pyran-2-yl] ester	ChEBI
dTDP-4-Dehydro-2,3,6-trideoxy-alpha-D-hexopyranose	Kegg
dTDP-4-Dehydro-2,3,6-trideoxy-a-D-hexopyranose	Generator
dTDP-4-Dehydro-2,3,6-trideoxy-α-D-hexopyranose	Generator
dTDP-4-Dehydro-2,3,6-trideoxy-a-D-glucose	Generator
dTDP-4-Dehydro-2,3,6-trideoxy-α-D-glucose	Generator

Chemical Formula

C₁₆H₂₄N₂O₁₃P₂

Average Mass

514.3170 Da

Monoisotopic Mass

514.07536 Da

IUPAC Name

{[hydroxy({[(2R,6R)-6-methyl-5-oxooxan-2-yl]oxy})phosphoryl]oxy}({[(2R,3S,5R)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinic acid

Traditional Name

[hydroxy([(2R,6R)-6-methyl-5-oxooxan-2-yl]oxy)phosphoryl]oxy([(2R,3S,5R)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphinic acid

CAS Registry Number

Not Available

SMILES

C[C@H]1O[C@@H](CCC1=O)OP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)N1C=C(C)C(O)=NC1=O

InChI Identifier

InChI=1S/C16H24N2O13P2/c1-8-6-18(16(22)17-15(8)21)13-5-11(20)12(29-13)7-27-32(23,24)31-33(25,26)30-14-4-3-10(19)9(2)28-14/h6,9,11-14,20H,3-5,7H2,1-2H3,(H,23,24)(H,25,26)(H,17,21,22)/t9-,11+,12-,13-,14-/m1/s1

InChI Key

YINKRXMSCURQIS-RHZHCTOVSA-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
Apis cerana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine nucleotide sugars

Direct Parent

Pyrimidine nucleotide sugars

Alternative Parents

Substituents

Pyrimidine nucleotide sugar
Pyrimidine 2'-deoxyribonucleoside diphosphate
Organic pyrophosphate
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Pyrimidine
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Alkyl phosphate
Heteroaromatic compound
Tetrahydrofuran
Vinylogous amide
Lactam
Secondary alcohol
Urea
Ketone
Cyclic ketone
Oxacycle
Azacycle
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Alcohol
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine nucleotide-sugar (CHEBI:81461 )

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	-0.27	ChemAxon
pKa (Strongest Acidic)	1.74	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	210.95 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	104.88 m³·mol⁻¹	ChemAxon
Polarizability	43.52 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

30791516

KEGG Compound ID

C18032

BioCyc ID

CPD-13382

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46174038

PDB ID

Not Available

ChEBI ID

81461

Good Scents ID

Not Available

References

General References

Zhang Z, Fukuzaki T, Myers AG: Synthesis of D-Desosamine and Analogs by Rapid Assembly of 3-Amino Sugars. Angew Chem Int Ed Engl. 2016 Jan 11;55(2):523-7. doi: 10.1002/anie.201507357. Epub 2015 Nov 27. [PubMed:26612347 ]
Hong L, Zhao Z, Melancon CE 3rd, Zhang H, Liu HW: In vitro characterization of the enzymes involved in TDP-D-forosamine biosynthesis in the spinosyn pathway of Saccharopolyspora spinosa. J Am Chem Soc. 2008 Apr 9;130(14):4954-67. doi: 10.1021/ja0771383. Epub 2008 Mar 18. [PubMed:18345667 ]
LOTUS database [Link]

Showing NP-Card for [hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid (NP0218291)

MOL for NP0218291 ([hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid)

3D MOL for NP0218291 ([hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid)

3D SDF for NP0218291 ([hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid)

3D-SDF for NP0218291 ([hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid)

PDB for NP0218291 ([hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid)

3D PDB for NP0218291 ([hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid)

SMILES for NP0218291 ([hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid)

INCHI for NP0218291 ([hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid)

Structure for NP0218291 ([hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid)

3D Structure for NP0218291 ([hydroxy([(2r,3s,5r)-3-hydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphoryl]oxy([(2r,6r)-6-methyl-5-oxooxan-2-yl]oxy)phosphinic acid)