NP-MRD: Showing NP-Card for gdp glucose (NP0254351)

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Record Information

Version

2.0

Created at

2022-09-07 18:29:22 UTC

Updated at

2022-09-07 18:29:22 UTC

NP-MRD ID

NP0254351

Secondary Accession Numbers

None

Natural Product Identification

Common Name

gdp glucose

Description

GDP-glucose, also known as (GDP-GLC)1 or GDP-D-glucose, 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 glucose is found in Eremothecium ashbyi. gdp glucose was first documented in 1972 (PMID: 4658992). GDP-glucose is an extremely weak basic (essentially neutral) compound (based on its pKa) (PMID: 718943) (PMID: 6216107) (PMID: 25010571) (PMID: 5084789).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306302020252D          

 39 42  0  0  0  0            999 V2000
 9997.4509 9997.8324    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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10000.4660 9999.2734    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.1827 9999.6854    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10002.0976 9999.1627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.769610000.4019    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.595710000.4019    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.0106 9999.6875    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10003.7252 9999.2775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  3  4  1  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652306302020252D          

 39 42  0  0  0  0            999 V2000
 9997.4509 9997.8324    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0254351

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC2=C(N=CN2[C@@H]2O[C@H](COP(O)(=O)OP(O)(=O)O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H]2O)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5-,7-,8-,9+,10-,11-,14-,15-/m1/s1

> <INCHI_KEY>
MVMSCBBUIHUTGJ-LRJDVEEWSA-N

> <FORMULA>
C16H25N5O16P2

> <MOLECULAR_WEIGHT>
605.3411

> <EXACT_MASS>
605.077152801

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
48.04960643089578

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphinic acid

> <ALOGPS_LOGP>
-1.76

> <JCHEM_LOGP>
-5.287584132999999

> <ALOGPS_LOGS>
-1.89

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.176324364365109

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7325998238285534

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6484093801081894

> <JCHEM_POLAR_SURFACE_AREA>
327.4299999999999

> <JCHEM_REFRACTIVITY>
118.51129999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.77e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gdp-α-D-glucose

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUN-20         0                                  
HETATM    1  O   UNK     0    8661.9088662.620   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8665.2538662.605   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8666.2028666.079   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8667.5378665.310   0.000  0.00  0.00           O+0
HETATM    5  P   UNK     0    8668.8748666.079   0.000  0.00  0.00           P+0
HETATM    6  O   UNK     0    8670.5828665.104   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8668.1038667.417   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0    8669.6458667.417   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0    8672.2868666.083   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0    8673.6208665.318   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8671.5198667.425   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    8673.0618667.425   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8676.2928663.776   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0    8676.2928669.942   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0    8678.9648665.318   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0    8677.6308670.709   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0    8678.9648668.400   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0    8663.6118666.232   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0    8662.8418663.862   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8664.3818663.862   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8664.8578665.326   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8676.2938668.396   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0    8674.9608667.626   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0    8674.9608666.086   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0    8676.2938665.316   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0    8677.6278666.086   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0    8677.6278667.626   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0    8657.0888666.286   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0    8656.6128664.821   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0    8657.6438663.677   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0    8659.1498663.997   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0    8659.6258665.462   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0    8658.5958666.606   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0    8661.0328666.088   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0    8660.8718667.620   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0    8659.3658667.940   0.000  0.00  0.00           N+0
HETATM   37  O   UNK     0    8656.0588667.431   0.000  0.00  0.00           O+0
HETATM   38  N   UNK     0    8657.1678662.212   0.000  0.00  0.00           N+0
HETATM   39  C   UNK     0    8662.3658665.318   0.000  0.00  0.00           C+0
CONECT    1   19                                                            
CONECT    2   20                                                            
CONECT    3    4   21                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7    8                                             
CONECT    6    5    9                                                       
CONECT    7    5                                                            
CONECT    8    5                                                            
CONECT    9    6   10   11   12                                             
CONECT   10    9   24                                                       
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13   25                                                            
CONECT   14   16   22                                                       
CONECT   15   26                                                            
CONECT   16   14                                                            
CONECT   17   27                                                            
CONECT   18   21   39                                                       
CONECT   19   20    1   39                                                  
CONECT   20   19   21    2                                                  
CONECT   21   20   18    3                                                  
CONECT   22   27   23   14                                                  
CONECT   23   22   24                                                       
CONECT   24   25   23   10                                                  
CONECT   25   24   26   13                                                  
CONECT   26   25   27   15                                                  
CONECT   27   22   26   17                                                  
CONECT   28   33   29   37                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   38                                                  
CONECT   31   30   32                                                       
CONECT   32   33   34   31                                                  
CONECT   33   28   32   36                                                  
CONECT   34   35   32   39                                                  
CONECT   35   36   34                                                       
CONECT   36   35   33                                                       
CONECT   37   28                                                            
CONECT   38   30                                                            
CONECT   39   34   19   18                                                  
MASTER        0    0    0    0    0    0    0    0   39    0   84    0
END

View in JSmol

Synonyms

Value	Source
(GDP-GLC)1	ChEBI
GDP-D-glucose	ChEBI
GDPG	ChEBI
Guanosine diphosphate glucose	ChEBI
Guanosine diphosphoglucose	ChEBI
Guanosine diphosphoric acid glucose	Generator
GDP-alpha-D-glucose	HMDB
Guanosine 5-pyrophosphate	HMDB
P-alpha-D-Glucopyranosyl ester	HMDB
GDP Glucose	MeSH, HMDB
Guanosine diphosphate glucose, (D)-isomer	MeSH, HMDB
GDP-glucose	ChEBI
GDP-a-D-Glucose	Generator, HMDB
GDP-α-D-glucose	Generator, HMDB
Guanosine 5'-diphosphate glucose	HMDB
Guanosine 5'-diphosphate-D-glucose	HMDB
Guanosine 5’-diphosphate glucose	HMDB
Guanosine 5’-diphosphate-D-glucose	HMDB
Guanosine diphosphate D-glucose	HMDB
Guanosine 5'-(trihydrogen diphosphate), P'-a-D-glucopyranosyl ester	HMDB
Guanosine 5'-(trihydrogen diphosphate), P'-alpha-D-glucopyranosyl ester	HMDB
Guanosine 5'-(trihydrogen diphosphate), P'-α-D-glucopyranosyl ester	HMDB
Guanosine 5'-(trihydrogen diphosphoric acid), P'-a-D-glucopyranosyl ester	HMDB
Guanosine 5'-(trihydrogen diphosphoric acid), P'-alpha-D-glucopyranosyl ester	HMDB
Guanosine 5'-(trihydrogen diphosphoric acid), P'-α-D-glucopyranosyl ester	HMDB
Guanosine 5’-(trihydrogen diphosphate), P’-a-D-glucopyranosyl ester	HMDB
Guanosine 5’-(trihydrogen diphosphate), P’-α-D-glucopyranosyl ester	HMDB
Guanosine 5’-(trihydrogen diphosphoric acid), P’-a-D-glucopyranosyl ester	HMDB
Guanosine 5’-(trihydrogen diphosphoric acid), P’-α-D-glucopyranosyl ester	HMDB

Chemical Formula

C₁₆H₂₅N₅O₁₆P₂

Average Mass

605.3411 Da

Monoisotopic Mass

605.07715 Da

IUPAC Name

[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphinic acid

Traditional Name

gdp-α-D-glucose

CAS Registry Number

Not Available

SMILES

NC1=NC2=C(N=CN2[C@@H]2O[C@H](COP(O)(=O)OP(O)(=O)O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H]2O)C(=O)N1

InChI Identifier

InChI=1S/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5-,7-,8-,9+,10-,11-,14-,15-/m1/s1

InChI Key

MVMSCBBUIHUTGJ-LRJDVEEWSA-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
Eremothecium ashbyi	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
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Alkyl phosphate
Pyrimidine
Vinylogous amide
Tetrahydrofuran
Azole
Imidazole
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Polyol
Azacycle
Oxacycle
Organopnictogen compound
Organic nitrogen compound
Alcohol
Amine
Hydrocarbon derivative
Organic oxide
Organonitrogen compound
Primary alcohol
Primary amine
Organooxygen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

GDP-D-glucose (CHEBI:62254 )

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	-5.3	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	327.43 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	118.51 m³·mol⁻¹	ChemAxon
Polarizability	48.05 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

HMDB0003351

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB023150

KNApSAcK ID

Not Available

Chemspider ID

559146

KEGG Compound ID

C00394

BioCyc ID

GDP-D-GLUCOSE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6900

PubChem Compound

644106

PDB ID

Not Available

ChEBI ID

62254

Good Scents ID

Not Available

References

General References

Chandra GR, Mandava N, Warthen JD Jr: Uridine diphosphate glucose:fatty acid glucosyl transferase activity of rape (Brassica napus L.) anther tissue. Biochim Biophys Acta. 1978 Oct 12;526(2):387-97. doi: 10.1016/0005-2744(78)90130-4. [PubMed:718943 ]
Orlean PA: (1,3)-beta-D-Glucan synthase from budding and filamentous cultures of the dimorphic fungus Candida albicans. Eur J Biochem. 1982 Oct;127(2):397-403. doi: 10.1111/j.1432-1033.1982.tb06885.x. [PubMed:6216107 ]
Chaleckis R, Ebe M, Pluskal T, Murakami I, Kondoh H, Yanagida M: Unexpected similarities between the Schizosaccharomyces and human blood metabolomes, and novel human metabolites. Mol Biosyst. 2014 Oct;10(10):2538-51. doi: 10.1039/c4mb00346b. [PubMed:25010571 ]
Heller JS, Villemez CL: Interaction of soluble glucosyl- and mannosyl-transferase enzyme activities in the synthesis of a glucomannan. Biochem J. 1972 Sep;129(3):645-55. doi: 10.1042/bj1290645. [PubMed:4658992 ]
Heller JS, Villemez CL: Solubilization of a mannose-polymerizing enzyme from Phaseolus aureus. Biochem J. 1972 Jun;128(2):243-52. doi: 10.1042/bj1280243. [PubMed:5084789 ]
LOTUS database [Link]

Showing NP-Card for gdp glucose (NP0254351)

MOL for NP0254351 (gdp glucose)

3D MOL for NP0254351 (gdp glucose)

3D SDF for NP0254351 (gdp glucose)

3D-SDF for NP0254351 (gdp glucose)

PDB for NP0254351 (gdp glucose)

3D PDB for NP0254351 (gdp glucose)

SMILES for NP0254351 (gdp glucose)

INCHI for NP0254351 (gdp glucose)

Structure for NP0254351 (gdp glucose)

3D Structure for NP0254351 (gdp glucose)