NP-MRD: Showing NP-Card for (2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0218034)

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Record Information

Version

2.0

Created at

2022-09-05 18:33:56 UTC

Updated at

2022-09-05 18:33:56 UTC

NP-MRD ID

NP0218034

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Description

5Alpha-[2-(beta-D-Glucopyranosyloxy)ethyl]-6-oxabicyclo[3.1.0]Hexane-1alpha,2beta-dimethanol belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. (2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol is found in Cerbera manghas. Based on a literature review very few articles have been published on 5alpha-[2-(beta-D-Glucopyranosyloxy)ethyl]-6-oxabicyclo[3.1.0]Hexane-1alpha,2beta-dimethanol.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309052220332D          

 24 26  0  0  1  0            999 V2000
    4.3675    4.3559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8825    3.6885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0620    3.7747    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5771    3.1073    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7566    3.1935    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2717    2.5261    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6073    1.7724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1224    1.1050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4579    0.3513    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2425    0.6062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7275   -0.0612    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2425   -0.7286    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4975   -1.5133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3044   -1.6848    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4579   -0.4737    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1224   -1.2274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3019   -1.3136    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7434   -0.0612    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4211    3.9472    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6006    4.0334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9060    4.6146    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5705    5.3683    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7265    4.5284    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2114    5.1958    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  9  8  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
 12 15  1  0  0  0  0
  9 15  1  0  0  0  0
 15 16  1  1  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
  9 18  1  0  0  0  0
  5 19  1  0  0  0  0
 19 20  1  6  0  0  0
 19 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
  3 23  1  0  0  0  0
 23 24  1  6  0  0  0
M  END


  Mrv1652309052220332D          

 24 26  0  0  1  0            999 V2000
    4.3675    4.3559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8825    3.6885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0620    3.7747    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5771    3.1073    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7566    3.1935    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2717    2.5261    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6073    1.7724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1224    1.1050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4579    0.3513    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2425    0.6062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7275   -0.0612    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2425   -0.7286    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4975   -1.5133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3044   -1.6848    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4579   -0.4737    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1224   -1.2274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3019   -1.3136    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7434   -0.0612    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4211    3.9472    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6006    4.0334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9060    4.6146    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5705    5.3683    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7265    4.5284    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2114    5.1958    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  9  8  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
 12 15  1  0  0  0  0
  9 15  1  0  0  0  0
 15 16  1  1  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
  9 18  1  0  0  0  0
  5 19  1  0  0  0  0
 19 20  1  6  0  0  0
 19 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
  3 23  1  0  0  0  0
 23 24  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0218034

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1CC[C@@]2(CCO[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O[C@@]12CO

> <INCHI_IDENTIFIER>
InChI=1S/C15H26O9/c16-5-8-1-2-14(15(8,7-18)24-14)3-4-22-13-12(21)11(20)10(19)9(6-17)23-13/h8-13,16-21H,1-7H2/t8-,9-,10-,11+,12-,13-,14+,15+/m1/s1

> <INCHI_KEY>
NPFGZJDRJCOHKS-OTLHJRDOSA-N

> <FORMULA>
C15H26O9

> <MOLECULAR_WEIGHT>
350.364

> <EXACT_MASS>
350.157682417

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
35.172158794689125

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S,6R)-2-{2-[(1S,4R,5R)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_LOGP>
-3.3507668033333333

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.165620420738076

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.206851075546643

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6365314347518103

> <JCHEM_POLAR_SURFACE_AREA>
152.37

> <JCHEM_REFRACTIVITY>
78.46990000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5S,6R)-2-{2-[(1S,4R,5R)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  O   UNK     0       8.153   8.131   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       7.247   6.885   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.716   7.046   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.811   5.800   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.279   5.961   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.374   4.715   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.000   3.308   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.095   2.063   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.721   0.656   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.186   1.132   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.091  -0.114   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.186  -1.360   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.662  -2.825   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       6.168  -3.145   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.721  -0.884   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.095  -2.291   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.563  -2.452   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.388  -0.114   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.653   7.368   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.121   7.529   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       3.558   8.614   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.932  10.021   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       5.089   8.453   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.995   9.699   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   23                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   19                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   15   18                                             
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12    9   16   18                                             
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15    9                                                       
CONECT   19    5   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21    3   24                                                  
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

View in JSmol

Synonyms

Value	Source
5a-[2-(b-D-Glucopyranosyloxy)ethyl]-6-oxabicyclo[3.1.0]hexane-1a,2b-dimethanol	Generator
5Α-[2-(β-D-glucopyranosyloxy)ethyl]-6-oxabicyclo[3.1.0]hexane-1α,2β-dimethanol	Generator

Chemical Formula

C₁₅H₂₆O₉

Average Mass

350.3640 Da

Monoisotopic Mass

350.15768 Da

IUPAC Name

(2R,3R,4S,5S,6R)-2-{2-[(1S,4R,5R)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

(2R,3R,4S,5S,6R)-2-{2-[(1S,4R,5R)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

OC[C@H]1CC[C@@]2(CCO[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O[C@@]12CO

InChI Identifier

InChI=1S/C15H26O9/c16-5-8-1-2-14(15(8,7-18)24-14)3-4-22-13-12(21)11(20)10(19)9(6-17)23-13/h8-13,16-21H,1-7H2/t8-,9-,10-,11+,12-,13-,14+,15+/m1/s1

InChI Key

NPFGZJDRJCOHKS-OTLHJRDOSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Cerbera manghas	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

Hexose monosaccharide
O-glycosyl compound
Monosaccharide
Oxane
Secondary alcohol
Polyol
Acetal
Organoheterocyclic compound
Oxacycle
Ether
Oxirane
Dialkyl ether
Hydrocarbon derivative
Alcohol
Primary alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	-3.4	ChemAxon
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	152.37 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	78.47 m³·mol⁻¹	ChemAxon
Polarizability	35.17 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

8840887

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10665534

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0218034)

MOL for NP0218034 ((2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0218034 ((2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0218034 ((2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0218034 ((2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0218034 ((2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0218034 ((2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0218034 ((2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0218034 ((2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0218034 ((2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0218034 ((2r,3r,4s,5s,6r)-2-{2-[(1s,4r,5r)-4,5-bis(hydroxymethyl)-6-oxabicyclo[3.1.0]hexan-1-yl]ethoxy}-6-(hydroxymethyl)oxane-3,4,5-triol)