NP-MRD: Showing NP-Card for (1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol (NP0291087)

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Record Information

Version

2.0

Created at

2022-09-09 22:03:01 UTC

Updated at

2022-09-09 22:03:01 UTC

NP-MRD ID

NP0291087

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol

Description

(1S,2S,5S,6R)-1-[(3R)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]Hept-3-ene-2,5-diol belongs to the class of organic compounds known as ynones. These are organic compounds containing the ynone functional group, an alpha,beta unsaturated ketone group with the general structure RC#C-C(=O)R' (R' not H). Based on a literature review very few articles have been published on (1S,2S,5S,6R)-1-[(3R)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]Hept-3-ene-2,5-diol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102200032D          

 15 16  0  0  1  0            999 V2000
   -1.9987   -3.6829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5862   -2.9684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7612   -2.9684    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3487   -3.6829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3487   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0638   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4763   -0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2382   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4763   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1908    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1908    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9053   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9053   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1908   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1908   -2.0625    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  1  0  0  0
  3  5  1  0  0  0  0
  5  6  3  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  9  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
  7 14  1  0  0  0  0
 14 15  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0291087

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H](O)C#C[C@@]12O[C@@H]1[C@@H](O)C=C[C@@H]2O

> <INCHI_IDENTIFIER>
InChI=1S/C10H12O5/c11-5-6(12)3-4-10-8(14)2-1-7(13)9(10)15-10/h1-2,6-9,11-14H,5H2/t6-,7+,8+,9-,10+/m1/s1

> <INCHI_KEY>
JWTSHQHIVXHRCI-KBDSZGMXSA-N

> <FORMULA>
C10H12O5

> <MOLECULAR_WEIGHT>
212.201

> <EXACT_MASS>
212.068473486

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
20.665499755191206

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,5S,6R)-1-[(3R)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol

> <JCHEM_LOGP>
-1.7552447680000005

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.20833103036139

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.598722700273576

> <JCHEM_PKA_STRONGEST_BASIC>
-3.110219674764707

> <JCHEM_POLAR_SURFACE_AREA>
93.45

> <JCHEM_REFRACTIVITY>
51.3663

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,5S,6R)-1-[(3R)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  O   UNK     0      -3.731  -6.875   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.961  -5.541   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.421  -5.541   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.651  -6.875   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -0.651  -4.207   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.119  -2.874   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.889  -1.540   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.445  -0.770   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.889  -0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.223   0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.223   2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       3.556  -0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.556  -1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.223  -2.310   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.223  -3.850   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                                                       
CONECT    7    6    8    9   14                                             
CONECT    8    7    9                                                       
CONECT    9    8    7   10                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    7   15                                                  
CONECT   15   14                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₂O₅

Average Mass

212.2010 Da

Monoisotopic Mass

212.06847 Da

IUPAC Name

(1S,2S,5S,6R)-1-[(3R)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol

Traditional Name

(1S,2S,5S,6R)-1-[(3R)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol

CAS Registry Number

Not Available

SMILES

OC[C@H](O)C#C[C@@]12O[C@@H]1[C@@H](O)C=C[C@@H]2O

InChI Identifier

InChI=1S/C10H12O5/c11-5-6(12)3-4-10-8(14)2-1-7(13)9(10)15-10/h1-2,6-9,11-14H,5H2/t6-,7+,8+,9-,10+/m1/s1

InChI Key

JWTSHQHIVXHRCI-KBDSZGMXSA-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 ynones. These are organic compounds containing the ynone functional group, an alpha,beta unsaturated ketone group with the general structure RC#C-C(=O)R' (R' not H).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Ynones

Alternative Parents

Substituents

Ynone
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Hydrocarbon derivative
Primary alcohol
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	-1.8	ChemAxon
pKa (Strongest Acidic)	12.6	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	93.45 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	51.37 m³·mol⁻¹	ChemAxon
Polarizability	20.67 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

162847657

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol (NP0291087)

MOL for NP0291087 ((1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol)

3D MOL for NP0291087 ((1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol)

3D SDF for NP0291087 ((1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol)

3D-SDF for NP0291087 ((1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol)

PDB for NP0291087 ((1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol)

3D PDB for NP0291087 ((1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol)

SMILES for NP0291087 ((1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol)

INCHI for NP0291087 ((1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol)

Structure for NP0291087 ((1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol)

3D Structure for NP0291087 ((1s,2s,5s,6r)-1-[(3r)-3,4-dihydroxybut-1-yn-1-yl]-7-oxabicyclo[4.1.0]hept-3-ene-2,5-diol)