NP-MRD: Showing NP-Card for (4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one (NP0226433)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-06 05:28:24 UTC

Updated at

2022-09-06 05:28:25 UTC

NP-MRD ID

NP0226433

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one

Description

Leiocarpin C belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety. (4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one was first documented in 2006 (PMID: 16819228). Based on a literature review very few articles have been published on Leiocarpin C.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309062207282D          

 18 19  0  0  1  0            999 V2000
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  0  0  0  0
  7  8  1  6  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  6  0  0  0
 10 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
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 12 17  1  0  0  0  0
  7 18  1  0  0  0  0
  2 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0226433

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]([C@H](O)C1=CC=CC=C1)[C@H]1C[C@@H](O)CC(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C13H16O5/c14-9-6-10(18-11(15)7-9)13(17)12(16)8-4-2-1-3-5-8/h1-5,9-10,12-14,16-17H,6-7H2/t9-,10-,12-,13+/m1/s1

> <INCHI_KEY>
XMOGEOVHRGIFNH-WFFHOREQSA-N

> <FORMULA>
C13H16O5

> <MOLECULAR_WEIGHT>
252.266

> <EXACT_MASS>
252.099773615

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
24.968347526865504

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4R,6R)-6-[(1R,2R)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one

> <JCHEM_LOGP>
-0.18591479900000046

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.293871172949657

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.916006626520797

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8383841603313194

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
62.588800000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4R,6R)-6-[(1R,2R)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   18                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   18                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   12                                                       
CONECT   18    7    2                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₁₆O₅

Average Mass

252.2660 Da

Monoisotopic Mass

252.09977 Da

IUPAC Name

(4R,6R)-6-[(1R,2R)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one

Traditional Name

(4R,6R)-6-[(1R,2R)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one

CAS Registry Number

Not Available

SMILES

O[C@H]([C@H](O)C1=CC=CC=C1)[C@H]1C[C@@H](O)CC(=O)O1

InChI Identifier

InChI=1S/C13H16O5/c14-9-6-10(18-11(15)7-9)13(17)12(16)8-4-2-1-3-5-8/h1-5,9-10,12-14,16-17H,6-7H2/t9-,10-,12-,13+/m1/s1

InChI Key

XMOGEOVHRGIFNH-WFFHOREQSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Delta valerolactones

Direct Parent

Delta valerolactones

Alternative Parents

Substituents

Delta valerolactone
Delta_valerolactone
Monocyclic benzene moiety
Benzenoid
Oxane
1,2-diol
Carboxylic acid ester
Secondary alcohol
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Organic oxygen compound
Organooxygen compound
Aromatic alcohol
Hydrocarbon derivative
Carbonyl group
Organic oxide
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	-0.19	ChemAxon
pKa (Strongest Acidic)	12.92	ChemAxon
pKa (Strongest Basic)	-2.8	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	3	ChemAxon
Refractivity	62.59 m³·mol⁻¹	ChemAxon
Polarizability	24.97 Å³	ChemAxon
Number of Rings	2	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

C00030651

Chemspider ID

10227718

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21599261

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Lan YH, Chang FR, Yang YL, Wu YC: New constituents from stems of Goniothalamus amuyon. Chem Pharm Bull (Tokyo). 2006 Jul;54(7):1040-3. doi: 10.1248/cpb.54.1040. [PubMed:16819228 ]
LOTUS database [Link]

Showing NP-Card for (4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one (NP0226433)

MOL for NP0226433 ((4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one)

3D MOL for NP0226433 ((4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one)

3D SDF for NP0226433 ((4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one)

3D-SDF for NP0226433 ((4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one)

PDB for NP0226433 ((4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one)

3D PDB for NP0226433 ((4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one)

SMILES for NP0226433 ((4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one)

INCHI for NP0226433 ((4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one)

Structure for NP0226433 ((4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one)

3D Structure for NP0226433 ((4r,6r)-6-[(1r,2r)-1,2-dihydroxy-2-phenylethyl]-4-hydroxyoxan-2-one)