NP-MRD: Showing NP-Card for [(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid (NP0288400)

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Record Information

Version

2.0

Created at

2022-09-09 18:05:00 UTC

Updated at

2022-09-09 18:05:00 UTC

NP-MRD ID

NP0288400

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid

Description

[(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid is found in Arabidopsis thaliana.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 08131209232D          

 42 43  0  0  0  0            999 V2000
    8.2828    3.1714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    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
    7.0717    2.8941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7729    4.7407    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.2432    3.7011    0.0000 C   0  0  2  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  2  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  2  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
    8.0278    3.9561    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 N   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
    6.9659    4.9122    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6301    4.2531    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
    9.1555    5.8249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7910    4.8464    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1770    5.1895    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
    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
    4.3748    0.5154    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
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8125    4.2110    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
    8.9840    5.0180    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
    6.1155    1.8322    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.2612    0.2633    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8563    3.1491    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3138    0.5418    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9547    0.2683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5238   -1.2021    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  7  4  1  1  0  0  0
  8  5  1  0  0  0  0
  9  2  1  0  0  0  0
 10  7  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 14  1  1  1  0  0  0
 14  6  1  0  0  0  0
 14  8  1  0  0  0  0
 15  9  2  0  0  0  0
 16  9  1  0  0  0  0
 16 13  2  0  0  0  0
 17  3  1  0  0  0  0
 12 17  1  1  0  0  0
 17 13  1  0  0  0  0
 18  6  1  0  0  0  0
  8 19  1  6  0  0  0
 10 20  1  6  0  0  0
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 22 13  1  0  0  0  0
 30  4  1  0  0  0  0
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 32 12  1  0  0  0  0
 14 33  1  6  0  0  0
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  7 38  1  6  0  0  0
  8 39  1  6  0  0  0
 10 40  1  1  0  0  0
 11 41  1  1  0  0  0
 12 42  1  6  0  0  0
M  END

     RDKit          3D

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    5.2186   -0.5927   -0.2169 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3074    0.0169   -1.0452 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0551   -0.2952   -0.5566 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0925    0.8785   -0.7817 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8748    0.4981   -0.2736 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3154    1.6602   -0.4290 P   0  0  1  0  0  5  0  0  0  0  0  0
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   -5.3858    2.3166    1.6236 O   0  0  0  0  0  0  0  0  0  0  0  0
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    5.2003   -1.0125    2.1606 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8487    0.9959   -1.0269 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7989    1.7256   -1.5793 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1341    1.3859   -1.1369 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.6970   -1.0428    0.5080 H   0  0  0  0  0  0  0  0  0  0  0  0
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    5.1337   -1.6890   -0.3184 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6980   -1.1871   -1.0798 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv0541 08131209232D          

 42 43  0  0  0  0            999 V2000
    8.2828    3.1714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 18  6  1  0  0  0  0
  8 19  1  6  0  0  0
 10 20  1  6  0  0  0
 11 21  1  6  0  0  0
 22 13  1  0  0  0  0
 30  4  1  0  0  0  0
 31  5  1  0  0  0  0
 32  7  1  0  0  0  0
 32 12  1  0  0  0  0
 14 33  1  6  0  0  0
 35 23  1  0  0  0  0
 35 24  1  0  0  0  0
 35 25  2  0  0  0  0
 35 33  1  0  0  0  0
 36 26  1  0  0  0  0
 36 27  2  0  0  0  0
 36 30  1  0  0  0  0
 36 34  1  0  0  0  0
 37 28  1  0  0  0  0
 37 29  2  0  0  0  0
 37 31  1  0  0  0  0
 37 34  1  0  0  0  0
  7 38  1  6  0  0  0
  8 39  1  6  0  0  0
 10 40  1  1  0  0  0
 11 41  1  1  0  0  0
 12 42  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0288400

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@](O)(COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(O)[C@]1([H])O)[C@](C)(CO)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H26N3O17P3/c1-14(6-18,33-35(23,24)25)8(19)5-31-37(28,29)34-36(26,27)30-4-7-10(20)11(21)12(32-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21H,4-6H2,1H3,(H,26,27)(H,28,29)(H2,15,16,22)(H2,23,24,25)/t7-,8-,10-,11-,12-,14+/m1/s1

> <INCHI_KEY>
HTJXTKBIUVFUAR-XHIBXCGHSA-N

> <FORMULA>
C14H26N3O17P3

> <MOLECULAR_WEIGHT>
601.2874

> <EXACT_MASS>
601.047505957

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
48.74194359302888

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2S,3R)-4-({[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-1,3-dihydroxy-2-methylbutan-2-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-1.13

> <JCHEM_LOGP>
-5.5237339314104

> <ALOGPS_LOGS>
-1.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.9134741150524555

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0509840675366178

> <JCHEM_PKA_STRONGEST_BASIC>
1.847721275379889

> <JCHEM_POLAR_SURFACE_AREA>
318.88000000000005

> <JCHEM_REFRACTIVITY>
125.91379999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.98e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2S,3R)-4-[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 13-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   35  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   36  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   37  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   38  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   39  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1   14                                                            
CONECT    2    3    9                                                       
CONECT    3    2   17                                                       
CONECT    4    7   30                                                       
CONECT    5    8   31                                                       
CONECT    6   14   18                                                       
CONECT    7    4   10   32   38                                             
CONECT    8    5   14   19   39                                             
CONECT    9    2   15   16                                                  
CONECT   10    7   11   20   40                                             
CONECT   11   10   12   21   41                                             
CONECT   12   11   17   32   42                                             
CONECT   13   16   17   22                                                  
CONECT   14    1    6    8   33                                             
CONECT   15    9                                                            
CONECT   16    9   13                                                       
CONECT   17    3   12   13                                                  
CONECT   18    6                                                            
CONECT   19    8                                                            
CONECT   20   10                                                            
CONECT   21   11                                                            
CONECT   22   13                                                            
CONECT   23   35                                                            
CONECT   24   35                                                            
CONECT   25   35                                                            
CONECT   26   36                                                            
CONECT   27   36                                                            
CONECT   28   37                                                            
CONECT   29   37                                                            
CONECT   30    4   36                                                       
CONECT   31    5   37                                                       
CONECT   32    7   12                                                       
CONECT   33   14   35                                                       
CONECT   34   36   37                                                       
CONECT   35   23   24   25   33                                             
CONECT   36   26   27   30   34                                             
CONECT   37   28   29   31   34                                             
CONECT   38    7                                                            
CONECT   39    8                                                            
CONECT   40   10                                                            
CONECT   41   11                                                            
CONECT   42   12                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   86    0
END

View in JSmol

Synonyms

Value	Source
2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol	ChEBI
4-CDP-2-C-Methyl-D-erythritol 2-phosphoric acid	Generator
4-Diphosphocytidyl-2C methylerythritol 2-phosphate	MeSH
4-DPCMEP	MeSH
4-Diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate	MeSH

Chemical Formula

C₁₄H₂₆N₃O₁₇P₃

Average Mass

601.2874 Da

Monoisotopic Mass

601.04751 Da

IUPAC Name

{[(2S,3R)-4-({[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-1,3-dihydroxy-2-methylbutan-2-yl]oxy}phosphonic acid

Traditional Name

[(2S,3R)-4-[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(O)[C@]1([H])O)[C@](C)(CO)OP(O)(O)=O

InChI Identifier

InChI=1S/C14H26N3O17P3/c1-14(6-18,33-35(23,24)25)8(19)5-31-37(28,29)34-36(26,27)30-4-7-10(20)11(21)12(32-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21H,4-6H2,1H3,(H,26,27)(H,28,29)(H2,15,16,22)(H2,23,24,25)/t7-,8-,10-,11-,12-,14+/m1/s1

InChI Key

HTJXTKBIUVFUAR-XHIBXCGHSA-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
Arabidopsis thaliana	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-5-phosphate
Pentose phosphate
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Monosaccharide phosphate
Organic pyrophosphate
Aminopyrimidine
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Phosphoric acid ester
Monosaccharide
Alkyl phosphate
Imidolactam
Pyrimidine
Organic phosphoric acid derivative
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organonitrogen compound
Organic nitrogen compound
Amine
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Primary amine
Primary alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

alditol 4-phosphate (CHEBI:16840 )
tetritol phosphate (CHEBI:16840 )
nucleotide-alditol (CHEBI:16840 )

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	-1.1	ALOGPS
logP	-5.5	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	1.05	ChemAxon
pKa (Strongest Basic)	1.85	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	318.88 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	125.91 m³·mol⁻¹	ChemAxon
Polarizability	48.74 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

Not Available

DrugBank ID

DB01859

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB030358

KNApSAcK ID

C00007621

Chemspider ID

Not Available

KEGG Compound ID

C11436

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

16840

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid (NP0288400)

MOL for NP0288400 ([(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid)

3D MOL for NP0288400 ([(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid)

3D SDF for NP0288400 ([(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid)

3D-SDF for NP0288400 ([(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid)

PDB for NP0288400 ([(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid)

3D PDB for NP0288400 ([(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid)

SMILES for NP0288400 ([(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid)

INCHI for NP0288400 ([(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid)

Structure for NP0288400 ([(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid)

3D Structure for NP0288400 ([(2s,3r)-4-[({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,3-dihydroxy-2-methylbutan-2-yl]oxyphosphonic acid)