NP-MRD: Showing NP-Card for (6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one (NP0244805)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-07 05:40:49 UTC

Updated at

2022-09-07 05:40:49 UTC

NP-MRD ID

NP0244805

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one

Description

Deacetylboronolide belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms. (6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one is found in Tetradenia riparia. (6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one was first documented in 2003 (PMID: 12737588). Based on a literature review very few articles have been published on Deacetylboronolide.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 34  0  0  0  0  0  0  0  0999 V2000
   -4.6295    0.9961   -0.6468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2088    0.4620   -0.8164 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9566   -0.4583    0.3500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5764   -1.0723    0.3226 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4922   -1.8962    1.4607 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4933   -0.0123    0.3987 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6824    0.7411    1.5409 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8283   -0.7392    0.3926 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9082   -1.4596   -0.7968 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0101    0.1846    0.4496 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2485   -0.6775    0.3375 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5026    0.0766    0.2409 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4928    1.2905   -0.2812 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2288    1.8367   -0.7430 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2093    2.9855   -1.2399 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0355    1.0948   -0.6392 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3010    0.1102   -0.5453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6553    1.5063    0.3353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9150    1.6617   -1.4792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2271   -0.1090   -1.7805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4785    1.2726   -0.8977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1589    0.0691    1.2891 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6966   -1.2814    0.2765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4518   -1.6924   -0.5684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1465   -2.7824    1.2666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5791    0.6643   -0.4742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1229    1.5324    1.6059 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8564   -1.3852    1.2756 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2525   -2.3523   -0.6176 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0528    0.7118    1.4254 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2220   -1.3729    1.2025 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0766   -1.3339   -0.5600 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4115   -0.3921    0.6061 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4361    1.8206   -0.3385 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 10  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  6
  5 25  1  0
  6 26  1  6
  7 27  1  0
  8 28  1  1
  9 29  1  0
 10 30  1  1
 11 31  1  0
 11 32  1  0
 12 33  1  0
 13 34  1  0
M  END


  Mrv1652309072207402D          

 16 16  0  0  1  0            999 V2000
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
 10  8  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 10 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0244805

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC[C@H](O)[C@@H](O)[C@@H](O)[C@H]1CC=CC(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C11H18O5/c1-2-4-7(12)10(14)11(15)8-5-3-6-9(13)16-8/h3,6-8,10-12,14-15H,2,4-5H2,1H3/t7-,8+,10+,11-/m0/s1

> <INCHI_KEY>
HFDOZMQUQOSBQC-URPMGSGRSA-N

> <FORMULA>
C11H18O5

> <MOLECULAR_WEIGHT>
230.26

> <EXACT_MASS>
230.11542368

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
23.446318151249223

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(6R)-6-[(1R,2R,3S)-1,2,3-trihydroxyhexyl]-5,6-dihydro-2H-pyran-2-one

> <JCHEM_LOGP>
0.3179380523333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.0501911679257

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.808446904489628

> <JCHEM_PKA_STRONGEST_BASIC>
-3.182279729192773

> <JCHEM_POLAR_SURFACE_AREA>
86.99

> <JCHEM_REFRACTIVITY>
57.4337

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(6R)-6-[(1R,2R,3S)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.002  -9.240   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      13.337  -7.700   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      13.337  -9.240   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.003 -10.010   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      12.003 -11.550   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      10.669  -9.240   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   10                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Value	Source
(+)-Deacetylboronolide	MeSH

Chemical Formula

C₁₁H₁₈O₅

Average Mass

230.2600 Da

Monoisotopic Mass

230.11542 Da

IUPAC Name

(6R)-6-[(1R,2R,3S)-1,2,3-trihydroxyhexyl]-5,6-dihydro-2H-pyran-2-one

Traditional Name

(6R)-6-[(1R,2R,3S)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one

CAS Registry Number

Not Available

SMILES

CCC[C@H](O)[C@@H](O)[C@@H](O)[C@H]1CC=CC(=O)O1

InChI Identifier

InChI=1S/C11H18O5/c1-2-4-7(12)10(14)11(15)8-5-3-6-9(13)16-8/h3,6-8,10-12,14-15H,2,4-5H2,1H3/t7-,8+,10+,11-/m0/s1

InChI Key

HFDOZMQUQOSBQC-URPMGSGRSA-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
Tetradenia riparia	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty alcohols

Direct Parent

Fatty alcohols

Alternative Parents

Substituents

Fatty alcohol
Dihydropyranone
Pyran
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Lactone
Secondary alcohol
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Polyol
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organooxygen compound
Alcohol
Organic oxygen compound
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	0.32	ChemAxon
pKa (Strongest Acidic)	12.81	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	57.43 m³·mol⁻¹	ChemAxon
Polarizability	23.45 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

101881300

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Chandrasekhar M, Chandra KL, Singh VK: Total synthesis of (+)-boronolide, (+)-deacetylboronolide, and (+)-dideacetylboronolide. J Org Chem. 2003 May 16;68(10):4039-45. doi: 10.1021/jo0269058. [PubMed:12737588 ]
LOTUS database [Link]

Showing NP-Card for (6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one (NP0244805)

MOL for NP0244805 ((6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one)

3D MOL for NP0244805 ((6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one)

3D SDF for NP0244805 ((6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one)

3D-SDF for NP0244805 ((6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one)

PDB for NP0244805 ((6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one)

3D PDB for NP0244805 ((6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one)

SMILES for NP0244805 ((6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one)

INCHI for NP0244805 ((6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one)

Structure for NP0244805 ((6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one)

3D Structure for NP0244805 ((6r)-6-[(1r,2r,3s)-1,2,3-trihydroxyhexyl]-5,6-dihydropyran-2-one)