NP-MRD: Showing NP-Card for (2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid (NP0323655)

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Record Information

Version

2.0

Created at

2022-09-12 03:13:24 UTC

Updated at

2022-09-12 03:13:24 UTC

NP-MRD ID

NP0323655

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid

Description

SCHEMBL17866929 belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds. (2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid is found in Bradyrhizobium japonicum. Based on a literature review very few articles have been published on SCHEMBL17866929.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122205132D          

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M  END

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M  END


  Mrv1652309122205132D          

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M  END
> <DATABASE_ID>
NP0323655

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H](O)[C@@H](O)[C@H](O[C@H]1O[C@@H]([C@H](O)[C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H]1O)C(O)=O)[C@H](O)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C18H30O17/c19-1-4(22)7(24)13(5(23)2-20)33-18-12(29)14(11(28)15(35-18)16(30)31)34-17-10(27)9(26)8(25)6(3-21)32-17/h2,4-15,17-19,21-29H,1,3H2,(H,30,31)/t4-,5-,6-,7-,8-,9+,10-,11-,12-,13-,14+,15+,17+,18+/m1/s1

> <INCHI_KEY>
DLQVOIRDGFAWPK-JUEBRVGPSA-N

> <FORMULA>
C18H30O17

> <MOLECULAR_WEIGHT>
518.421

> <EXACT_MASS>
518.148299506

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
46.375764415861255

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5R,6S)-3,5-dihydroxy-6-{[(2S,3S,4R,5R)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid

> <JCHEM_LOGP>
-6.789757316333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.839138002348468

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1887815517731366

> <JCHEM_PKA_STRONGEST_BASIC>
-3.651627905024575

> <JCHEM_POLAR_SURFACE_AREA>
293.59

> <JCHEM_REFRACTIVITY>
102.03960000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5R,6S)-3,5-dihydroxy-6-{[(2S,3S,4R,5R)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  O   UNK     0      -5.335  -9.240   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -4.001  -8.470   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -5.335  -6.160   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -2.667  -6.160   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -4.001  -3.850   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -5.335  -4.620   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -6.668  -3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -9.336  -3.850   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -8.002  -6.160   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -8.002  -1.540   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -5.335  -1.540   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -6.668   0.770   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -9.336   0.770   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0     -10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0     -12.003   0.770   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -9.336   2.310   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0     -10.669   3.080   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -8.002   3.080   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -8.002   4.620   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -5.335   3.080   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -2.667  -1.540   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -1.334  -8.470   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       0.000  -6.160   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       2.667  -6.160   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   30                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   28                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   13                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    9   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   28                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   26                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22   19   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   17   27                                                  
CONECT   27   26                                                            
CONECT   28   15    7   29                                                  
CONECT   29   28                                                            
CONECT   30    5   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₃₀O₁₇

Average Mass

518.4210 Da

Monoisotopic Mass

518.14830 Da

IUPAC Name

(2S,3R,4S,5R,6S)-3,5-dihydroxy-6-{[(2S,3S,4R,5R)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid

Traditional Name

(2S,3R,4S,5R,6S)-3,5-dihydroxy-6-{[(2S,3S,4R,5R)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

OC[C@@H](O)[C@@H](O)[C@H](O[C@H]1O[C@@H]([C@H](O)[C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H]1O)C(O)=O)[C@H](O)C=O

InChI Identifier

InChI=1S/C18H30O17/c19-1-4(22)7(24)13(5(23)2-20)33-18-12(29)14(11(28)15(35-18)16(30)31)34-17-10(27)9(26)8(25)6(3-21)32-17/h2,4-15,17-19,21-29H,1,3H2,(H,30,31)/t4-,5-,6-,7-,8-,9+,10-,11-,12-,13-,14+,15+,17+,18+/m1/s1

InChI Key

DLQVOIRDGFAWPK-JUEBRVGPSA-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
Bradyrhizobium japonicum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Oligosaccharides

Alternative Parents

Substituents

Oligosaccharide
Fatty acyl glycoside
1-o-glucuronide
O-glucuronide
Glucuronic acid or derivatives
Alkyl glycoside
Glycosyl compound
O-glycosyl compound
Fatty alcohol
Beta-hydroxy acid
Fatty acyl
Hydroxy acid
Pyran
Oxane
Alpha-hydroxyaldehyde
Secondary alcohol
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Acetal
Oxacycle
Carboxylic acid
Carboxylic acid derivative
Polyol
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Aldehyde
Primary alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	-6.8	ChemAxon
pKa (Strongest Acidic)	3.19	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	293.59 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	102.04 m³·mol⁻¹	ChemAxon
Polarizability	46.38 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

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

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

121434220

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid (NP0323655)

MOL for NP0323655 ((2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid)

3D MOL for NP0323655 ((2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid)

3D SDF for NP0323655 ((2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid)

3D-SDF for NP0323655 ((2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid)

PDB for NP0323655 ((2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid)

3D PDB for NP0323655 ((2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid)

SMILES for NP0323655 ((2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid)

INCHI for NP0323655 ((2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid)

Structure for NP0323655 ((2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid)

3D Structure for NP0323655 ((2s,3r,4s,5r,6s)-3,5-dihydroxy-6-{[(2s,3s,4r,5r)-2,4,5,6-tetrahydroxy-1-oxohexan-3-yl]oxy}-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxane-2-carboxylic acid)