NP-MRD: Showing NP-Card for {[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid (NP0322861)

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Record Information

Version

1.0

Created at

2022-09-12 01:54:13 UTC

Updated at

2022-09-12 01:54:13 UTC

NP-MRD ID

NP0322861

Secondary Accession Numbers

None

Natural Product Identification

Common Name

{[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid

Description

Adenosine 5'-diphosphate glucose belongs to the class of organic compounds known as 1-hydroxy-4-unsubstituted benzenoids. These are phenols that are unsubstituted at the 4-position. Adenosine 5'-diphosphate glucose is a strong basic compound (based on its pKa). Outside of the human body, Adenosine 5'-diphosphate glucose has been detected, but not quantified in, cereals and cereal products. {[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid is found in Arabidopsis thaliana. This could make adenosine 5'-diphosphate glucose a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652305221919592D          

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M  END

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M  END


  Mrv1652305221919592D          

 38 41  0  0  0  0            999 V2000
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 37 29  2  0  0  0  0
 37 32  1  0  0  0  0
 37 36  1  0  0  0  0
 38 30  1  0  0  0  0
 38 31  2  0  0  0  0
 38 35  1  0  0  0  0
 38 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0322861

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=C2N=CN(C3OC(COP(O)(=O)OP(O)(=O)OC4OC(CO)C(O)C(O)C4O)C(O)C3O)C2=NC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C16H25N5O15P2/c17-13-7-14(19-3-18-13)21(4-20-7)15-11(26)9(24)6(33-15)2-32-37(28,29)36-38(30,31)35-16-12(27)10(25)8(23)5(1-22)34-16/h3-6,8-12,15-16,22-27H,1-2H2,(H,28,29)(H,30,31)(H2,17,18,19)

> <INCHI_KEY>
WFPZSXYXPSUOPY-UHFFFAOYSA-N

> <FORMULA>
C16H25N5O15P2

> <MOLECULAR_WEIGHT>
589.3417

> <EXACT_MASS>
589.082238179

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
50.2946159303453

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphinic acid

> <ALOGPS_LOGP>
-1.76

> <JCHEM_LOGP>
-6.7725679530330645

> <ALOGPS_LOGS>
-2.09

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.107282857130618

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7298676687415737

> <JCHEM_PKA_STRONGEST_BASIC>
3.9931246302818533

> <JCHEM_POLAR_SURFACE_AREA>
311.75000000000006

> <JCHEM_REFRACTIVITY>
117.08579999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.84e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0     -13.079  -3.278   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.061  -2.789   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -11.672  -3.904   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.185  -1.884   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -11.511  -5.436   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.650  -2.359   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0     -10.104  -6.062   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.555  -1.114   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -8.858  -5.157   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -9.019  -3.625   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       4.924   5.923   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0       6.258   3.613   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0       4.924   1.303   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0     -14.325  -4.183   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0     -12.757  -6.341   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       2.126  -3.824   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -9.943  -7.594   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       4.095  -1.114   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -7.451  -5.783   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -4.619  -1.822   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -2.808  -4.313   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -5.740  -1.940   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -6.993  -4.753   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -2.468  -2.162   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       0.185  -0.344   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0     -10.426  -2.999   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -7.773  -2.720   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -4.959  -3.973   0.000  0.00  0.00           O+0
HETATM   37  P   UNK     0      -3.714  -3.068   0.000  0.00  0.00           P+0
HETATM   38  P   UNK     0      -6.366  -3.346   0.000  0.00  0.00           P+0
CONECT    1    5   22                                                       
CONECT    2    6   32                                                       
CONECT    3   18   19                                                       
CONECT    4   20   21                                                       
CONECT    5    1    8   34                                                  
CONECT    6    2    9   33                                                  
CONECT    7   13   14   20                                                  
CONECT    8    5   10   23                                                  
CONECT    9    6   11   24                                                  
CONECT   10    8   12   25                                                  
CONECT   11    9   15   26                                                  
CONECT   12   10   16   27                                                  
CONECT   13    7   17   18                                                  
CONECT   14    7   19   21                                                  
CONECT   15   11   21   33                                                  
CONECT   16   12   34   35                                                  
CONECT   17   13                                                            
CONECT   18    3   13                                                       
CONECT   19    3   14                                                       
CONECT   20    4    7                                                       
CONECT   21    4   14   15                                                  
CONECT   22    1                                                            
CONECT   23    8                                                            
CONECT   24    9                                                            
CONECT   25   10                                                            
CONECT   26   11                                                            
CONECT   27   12                                                            
CONECT   28   37                                                            
CONECT   29   37                                                            
CONECT   30   38                                                            
CONECT   31   38                                                            
CONECT   32    2   37                                                       
CONECT   33    6   15                                                       
CONECT   34    5   16                                                       
CONECT   35   16   38                                                       
CONECT   36   37   38                                                       
CONECT   37   28   29   32   36                                             
CONECT   38   30   31   35   36                                             
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Value	Source
Adenosine 5'-diphosphoric acid glucose	Generator
Diphosphate glucose, adenosine	MeSH
Glucose, ADP	MeSH
Pyrophosphateglucose, adenosine	MeSH
ADP Glucose	MeSH
Diphosphoglucose, adenosine	MeSH
ADPG	MeSH
Adenosine diphosphate glucose	MeSH
Adenosine diphosphoglucose	MeSH
Adenosine pyrophosphateglucose	MeSH
Glucose, adenosine diphosphate	MeSH

Chemical Formula

C₁₆H₂₅N₅O₁₅P₂

Average Mass

589.3417 Da

Monoisotopic Mass

589.08224 Da

IUPAC Name

[({[5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphinic acid

Traditional Name

{[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid

CAS Registry Number

Not Available

SMILES

NC1=C2N=CN(C3OC(COP(O)(=O)OP(O)(=O)OC4OC(CO)C(O)C(O)C4O)C(O)C3O)C2=NC=N1

InChI Identifier

InChI=1S/C16H25N5O15P2/c17-13-7-14(19-3-18-13)21(4-20-7)15-11(26)9(24)6(33-15)2-32-37(28,29)36-38(30,31)35-16-12(27)10(25)8(23)5(1-22)34-16/h3-6,8-12,15-16,22-27H,1-2H2,(H,28,29)(H,30,31)(H2,17,18,19)

InChI Key

WFPZSXYXPSUOPY-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
Arabidopsis thaliana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1-hydroxy-4-unsubstituted benzenoids. These are phenols that are unsubstituted at the 4-position.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Phenols

Sub Class

1-hydroxy-4-unsubstituted benzenoids

Direct Parent

1-hydroxy-4-unsubstituted benzenoids

Alternative Parents

Substituents

1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Monocyclic benzene moiety
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic 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	-1.8	ALOGPS
logP	-6.8	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	3.99	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	311.75 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	117.09 m³·mol⁻¹	ChemAxon
Polarizability	50.29 Å³	ChemAxon
Number of Rings	4	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

HMDB0062621

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB001211

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

198

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for {[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid (NP0322861)

MOL for NP0322861 ({[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

3D MOL for NP0322861 ({[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

3D SDF for NP0322861 ({[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

3D-SDF for NP0322861 ({[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

PDB for NP0322861 ({[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

3D PDB for NP0322861 ({[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

SMILES for NP0322861 ({[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

INCHI for NP0322861 ({[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

Structure for NP0322861 ({[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

3D Structure for NP0322861 ({[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)