NP-MRD: Showing NP-Card for D-Vacciniin (NP0336053)

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Record Information

Version

2.0

Created at

2024-09-11 04:31:25 UTC

Updated at

2024-09-11 04:31:25 UTC

NP-MRD ID

NP0336053

Secondary Accession Numbers

None

Natural Product Identification

Common Name

D-Vacciniin

Description

D-Vacciniin belongs to the class of organic compounds known as benzoic acid esters. These are ester derivatives of benzoic acid. Based on a literature review very few articles have been published on D-Vacciniin.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05262307032D          

 20 21  0  0  0  0            999 V2000
   -0.5009    4.7143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2154    4.3018    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2154    3.4768    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5009    3.0643    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2136    3.4768    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2136    4.3018    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9280    4.7143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9280    3.0643    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5009    2.2393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9298    3.0643    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9298    4.7143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8818    3.5873    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4693    2.8728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8818    2.1584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7068    2.1583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1193    2.8728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7068    3.5873    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4693    4.3018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8818    5.0163    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6443    4.3018    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  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  6  0  0  0
  5  8  1  6  0  0  0
  4  9  1  1  0  0  0
  3 10  1  6  0  0  0
  2 11  1  1  0  0  0
 11 20  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
 12 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0336053

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1O[C@H](COC(=O)C2=CC=CC=C2)[C@@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1/C13H16O7/c14-9-8(20-13(18)11(16)10(9)15)6-19-12(17)7-4-2-1-3-5-7/h1-5,8-11,13-16,18H,6H2/t8-,9-,10+,11-,13+/s2

> <INCHI_KEY>
MRDRXKCKIMVUHN-QRWDNLJCNA-N

> <FORMULA>
C13H16O7

> <MOLECULAR_WEIGHT>
284.264

> <EXACT_MASS>
284.089602855

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
27.353361679901447

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4S,5R,6S)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl benzoate

> <JCHEM_LOGP>
-0.4372393693333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.692118057207127

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.298285318132871

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6490839182544597

> <JCHEM_POLAR_SURFACE_AREA>
116.45

> <JCHEM_REFRACTIVITY>
65.74540000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5R,6S)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl benzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-23         0                                  
HETATM    1  O   UNK     0      -0.935   8.800   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.269   8.030   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.269   6.490   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.935   5.720   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.399   6.490   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.399   8.030   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.732   8.800   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.732   5.720   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -0.935   4.180   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -3.602   5.720   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -3.602   8.800   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -7.246   6.696   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.476   5.363   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -7.246   4.029   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -8.786   4.029   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -9.556   5.363   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -8.786   6.696   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.476   8.030   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -7.246   9.364   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -4.936   8.030   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   11                                                  
CONECT    3    2    4   10                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5                                                            
CONECT    9    4                                                            
CONECT   10    3                                                            
CONECT   11    2   20                                                       
CONECT   12   13   17   18                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   12                                                       
CONECT   18   12   19   20                                                  
CONECT   19   18                                                            
CONECT   20   11   18                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₁₆O₇

Average Mass

284.2640 Da

Monoisotopic Mass

284.08960 Da

IUPAC Name

[(2R,3S,4S,5R,6S)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl benzoate

Traditional Name

[(2R,3S,4S,5R,6S)-3,4,5,6-tetrahydroxyoxan-2-yl]methyl benzoate

CAS Registry Number

Not Available

SMILES

O[C@H]1O[C@H](COC(=O)C2=CC=CC=C2)[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1/C13H16O7/c14-9-8(20-13(18)11(16)10(9)15)6-19-12(17)7-4-2-1-3-5-7/h1-5,8-11,13-16,18H,6H2/t8-,9-,10+,11-,13+/s2

InChI Key

MRDRXKCKIMVUHN-QRWDNLJCNA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as benzoic acid esters. These are ester derivatives of benzoic acid.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Benzoic acid esters

Alternative Parents

Substituents

Benzoate ester
Benzoyl
Monosaccharide
Oxane
Carboxylic acid ester
Hemiacetal
Secondary alcohol
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Organooxygen compound
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	-0.44	ChemAxon
pKa (Strongest Acidic)	11.3	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.45 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	65.75 m³·mol⁻¹	ChemAxon
Polarizability	27.35 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for D-Vacciniin (NP0336053)

MOL for NP0336053 (D-Vacciniin)

3D MOL for NP0336053 (D-Vacciniin)

3D SDF for NP0336053 (D-Vacciniin)

3D-SDF for NP0336053 (D-Vacciniin)

PDB for NP0336053 (D-Vacciniin)

3D PDB for NP0336053 (D-Vacciniin)

SMILES for NP0336053 (D-Vacciniin)

INCHI for NP0336053 (D-Vacciniin)

Structure for NP0336053 (D-Vacciniin)

3D Structure for NP0336053 (D-Vacciniin)