NP-MRD: Showing NP-Card for methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate (NP0253089)

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Record Information

Version

2.0

Created at

2022-09-07 16:51:06 UTC

Updated at

2022-09-07 16:51:06 UTC

NP-MRD ID

NP0253089

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate

Description

Methyl 2-[(2R,4S,5S,6S)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate belongs to the class of organic compounds known as c-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a C-glycosidic bond. methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate is found in Goniothalamus amuyon. Based on a literature review very few articles have been published on methyl 2-[(2R,4S,5S,6S)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 38  0  0  0  0  0  0  0  0999 V2000
    5.3832   -1.6326    0.8154 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0088   -1.5667    1.0948 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1318   -0.9040    0.2335 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5671   -0.3505   -0.8272 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6909   -0.8068    0.4889 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1780    0.5969    0.5261 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3831    1.3932   -0.7181 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3068    2.4682   -0.7549 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1873    2.9873    0.5372 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0107    1.7215   -1.0318 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0572    2.4574   -0.4822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8431    0.3485   -0.4395 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0845   -0.3772   -0.2038 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1020   -1.4541    0.6564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2597   -2.1788    0.9014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4082   -1.8126    0.2713 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4236   -0.7508   -0.5864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2498   -0.0276   -0.8243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1890    0.5311    0.7970 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4927   -1.5593   -0.3069 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7270   -2.6281    1.1769 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8756   -0.8150    1.3498 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1699   -1.4675   -0.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5030   -1.2405    1.5135 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7019    1.1163    1.3704 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3926    0.8268   -1.6520 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3634    1.9479   -0.6471 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5006    3.2542   -1.5016 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7682    3.2301    0.7356 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1062    1.6809   -2.1307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4270    2.1038    0.3346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2288   -0.2478   -1.1319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2146   -1.7756    1.1771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2370   -3.0208    1.5985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3170   -2.3660    0.4539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3401   -0.4800   -1.0703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2971    0.7982   -1.5125 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 19  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 19  6  1  0
 18 13  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  1
  7 26  1  0
  7 27  1  0
  8 28  1  6
  9 29  1  0
 10 30  1  6
 11 31  1  0
 12 32  1  6
 14 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  0
 18 37  1  0
M  END


  Mrv1652309072218512D          

 19 20  0  0  1  0            999 V2000
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    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   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   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
   -2.1434   -3.7125    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
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    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  2  0  0  0  0
  3  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  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  1  6  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
 12 19  1  0  0  0  0
  6 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0253089

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C14H18O5/c1-18-12(16)8-10-7-11(15)13(17)14(19-10)9-5-3-2-4-6-9/h2-6,10-11,13-15,17H,7-8H2,1H3/t10-,11+,13+,14+/m1/s1

> <INCHI_KEY>
KDINCHVBSLYDMN-XWUBHJNHSA-N

> <FORMULA>
C14H18O5

> <MOLECULAR_WEIGHT>
266.293

> <EXACT_MASS>
266.11542368

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
27.07582057120405

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 2-[(2R,4S,5S,6S)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate

> <JCHEM_LOGP>
0.4572117046666663

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.916971522815754

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.064842106400384

> <JCHEM_PKA_STRONGEST_BASIC>
-3.223175115409539

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
67.34000000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl [(2R,4S,5S,6S)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate

> <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       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.000  -3.080   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                                                       
CONECT    6    5    7   19                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   19                                                  
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   13                                                       
CONECT   19   12    6                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

View in JSmol

Synonyms

Value	Source
Methyl 2-[(2R,4S,5S,6S)-4,5-dihydroxy-6-phenyloxan-2-yl]acetic acid	Generator

Chemical Formula

C₁₄H₁₈O₅

Average Mass

266.2930 Da

Monoisotopic Mass

266.11542 Da

IUPAC Name

methyl 2-[(2R,4S,5S,6S)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate

Traditional Name

methyl [(2R,4S,5S,6S)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C14H18O5/c1-18-12(16)8-10-7-11(15)13(17)14(19-10)9-5-3-2-4-6-9/h2-6,10-11,13-15,17H,7-8H2,1H3/t10-,11+,13+,14+/m1/s1

InChI Key

KDINCHVBSLYDMN-XWUBHJNHSA-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
Goniothalamus amuyon	LOTUS Database	35616633

Chemical Taxonomy

Description

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

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

C-glycosyl compounds

Alternative Parents

Substituents

C-glycosyl compound
Benzenoid
Oxane
Monosaccharide
Monocyclic benzene moiety
Methyl ester
Secondary alcohol
Carboxylic acid ester
1,2-diol
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Carboxylic acid derivative
Organic oxide
Hydrocarbon derivative
Carbonyl group
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	0.46	ChemAxon
pKa (Strongest Acidic)	13.06	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	67.34 m³·mol⁻¹	ChemAxon
Polarizability	27.08 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

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

162983830

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate (NP0253089)

MOL for NP0253089 (methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate)

3D MOL for NP0253089 (methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate)

3D SDF for NP0253089 (methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate)

3D-SDF for NP0253089 (methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate)

PDB for NP0253089 (methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate)

3D PDB for NP0253089 (methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate)

SMILES for NP0253089 (methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate)

INCHI for NP0253089 (methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate)

Structure for NP0253089 (methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate)

3D Structure for NP0253089 (methyl 2-[(2r,4s,5s,6s)-4,5-dihydroxy-6-phenyloxan-2-yl]acetate)