NP-MRD: Showing NP-Card for {[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid (NP0148970)

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Record Information

Version

1.0

Created at

2022-09-02 04:47:49 UTC

Updated at

2022-09-02 04:47:49 UTC

NP-MRD ID

NP0148970

Secondary Accession Numbers

None

Natural Product Identification

Common Name

{[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid

Description

GDP-L-fucose belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group. GDP-L-fucose is a strong basic compound (based on its pKa). Within humans, GDP-L-fucose participates in a number of enzymatic reactions. In particular, GDP-L-fucose can be converted into GDP-4-dehydro-6-deoxy-D-mannose through the action of the enzyme GDP-L-fucose synthase. In addition, GDP-L-fucose can be biosynthesized from fucose 1-phosphate through the action of the enzyme fucose-1-phosphate guanylyltransferase. In humans, GDP-L-fucose is involved in fructose intolerance, hereditary. Outside of the human body, GDP-L-fucose is found, on average, in the highest concentration within milk (cow). {[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid is found in Arabidopsis thaliana. This could make GDP-L-fucose a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652305221920472D          

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M  END

     RDKit          3D

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M  END


  Mrv1652305221920472D          

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 24  9  1  0  0  0  0
 25 10  1  0  0  0  0
 26 11  1  0  0  0  0
 27 13  1  0  0  0  0
 32  2  1  0  0  0  0
 33  4  1  0  0  0  0
 33 15  1  0  0  0  0
 34  5  1  0  0  0  0
 34 14  1  0  0  0  0
 35 15  1  0  0  0  0
 37 28  1  0  0  0  0
 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>
NP0148970

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1OC(OP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2O)N2C=NC3=C2NC(=N)N=C3O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C16H25N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,7-11,14-15,22-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)

> <INCHI_KEY>
LQEBEXMHBLQMDB-UHFFFAOYSA-N

> <FORMULA>
C16H25N5O15P2

> <MOLECULAR_WEIGHT>
589.3417

> <EXACT_MASS>
589.082238179

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
50.35778180019027

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy][(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]phosphinic acid

> <ALOGPS_LOGP>
-1.45

> <JCHEM_LOGP>
-4.7463169002200365

> <ALOGPS_LOGS>
-1.92

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.7816533430109756

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7078968338117804

> <JCHEM_PKA_STRONGEST_BASIC>
3.3839265821482374

> <JCHEM_POLAR_SURFACE_AREA>
308.19000000000005

> <JCHEM_REFRACTIVITY>
127.54869999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.02e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{[3,4-dihydroxy-5-(6-hydroxy-2-imino-3H-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-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     -10.769 -13.897   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.454  -6.934   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -9.362 -14.523   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.208  -6.029   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -9.201 -16.055   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.744  -6.505   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -7.794 -16.681   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.161  -5.259   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -6.548 -15.776   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.530   0.237   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.744  -4.013   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -6.709 -14.245   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.864  -2.073   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       5.198  -2.843   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0       2.530  -2.843   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       3.864  -0.533   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0      -0.268  -2.549   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0     -10.447 -16.960   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -0.268  -7.970   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -7.633 -18.213   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       1.701  -5.259   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -5.141 -16.403   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       2.530   1.777   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -5.444  -8.125   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -3.634 -10.617   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -7.156 -11.969   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -4.093 -11.647   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -3.293  -8.466   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -8.116 -13.618   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -2.208  -4.489   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -5.463 -13.339   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -5.785 -10.276   0.000  0.00  0.00           O+0
HETATM   37  P   UNK     0      -4.539  -9.371   0.000  0.00  0.00           P+0
HETATM   38  P   UNK     0      -5.624 -11.808   0.000  0.00  0.00           P+0
CONECT    1    4                                                            
CONECT    2    5   32                                                       
CONECT    3   18   21                                                       
CONECT    4    1    7   33                                                  
CONECT    5    2    8   34                                                  
CONECT    6   12   13   18                                                  
CONECT    7    4    9   22                                                  
CONECT    8    5   10   23                                                  
CONECT    9    7   11   24                                                  
CONECT   10    8   14   25                                                  
CONECT   11    9   15   26                                                  
CONECT   12    6   19   21                                                  
CONECT   13    6   20   27                                                  
CONECT   14   10   21   34                                                  
CONECT   15   11   33   35                                                  
CONECT   16   17   19   20                                                  
CONECT   17   16                                                            
CONECT   18    3    6                                                       
CONECT   19   12   16                                                       
CONECT   20   13   16                                                       
CONECT   21    3   12   14                                                  
CONECT   22    7                                                            
CONECT   23    8                                                            
CONECT   24    9                                                            
CONECT   25   10                                                            
CONECT   26   11                                                            
CONECT   27   13                                                            
CONECT   28   37                                                            
CONECT   29   37                                                            
CONECT   30   38                                                            
CONECT   31   38                                                            
CONECT   32    2   37                                                       
CONECT   33    4   15                                                       
CONECT   34    5   14                                                       
CONECT   35   15   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
Diphosphate fucose, guanosine	MeSH
Fucose, guanosine diphosphate	MeSH
Fucose, GDP	MeSH
Guanosine diphosphate fucose	MeSH
Guanosine diphosphofucose	MeSH
Diphosphofucose, guanosine	MeSH
GDP Fucose	MeSH

Chemical Formula

C₁₆H₂₅N₅O₁₅P₂

Average Mass

589.3417 Da

Monoisotopic Mass

589.08224 Da

IUPAC Name

[({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy][(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]phosphinic acid

Traditional Name

{[3,4-dihydroxy-5-(6-hydroxy-2-imino-3H-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid

CAS Registry Number

Not Available

SMILES

CC1OC(OP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2O)N2C=NC3=C2NC(=N)N=C3O)C(O)C(O)C1O

InChI Identifier

InChI=1S/C16H25N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,7-11,14-15,22-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)

InChI Key

LQEBEXMHBLQMDB-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 purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine nucleotide sugars

Direct Parent

Purine nucleotide sugars

Alternative Parents

Substituents

Purine nucleotide sugar
Purine ribonucleoside diphosphate
Purine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
6-oxopurine
Hypoxanthine
Monosaccharide phosphate
Organic pyrophosphate
Imidazopyrimidine
Purine
Aminopyrimidine
Monoalkyl phosphate
Pyrimidone
Pyrimidine
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Alkyl phosphate
Tetrahydrofuran
Vinylogous amide
Azole
Imidazole
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Azacycle
Polyol
Oxacycle
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Organopnictogen compound
Alcohol
Primary amine
Organonitrogen compound
Amine
Organic oxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	-1.4	ALOGPS
logP	-4.7	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.71	ChemAxon
pKa (Strongest Basic)	3.38	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	308.19 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	127.55 m³·mol⁻¹	ChemAxon
Polarizability	50.36 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB021816

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

451

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-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid (NP0148970)

MOL for NP0148970 ({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid)

3D MOL for NP0148970 ({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid)

3D SDF for NP0148970 ({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid)

3D-SDF for NP0148970 ({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid)

PDB for NP0148970 ({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid)

3D PDB for NP0148970 ({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid)

SMILES for NP0148970 ({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid)

INCHI for NP0148970 ({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid)

Structure for NP0148970 ({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid)

3D Structure for NP0148970 ({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3h-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy((3,4,5-trihydroxy-6-methyloxan-2-yl)oxy)phosphinic acid)