NP-MRD: Showing NP-Card for methyl (2r,3s)-3-nonyloxirane-2-carboxylate (NP0312608)

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Record Information

Version

2.0

Created at

2022-09-11 09:32:25 UTC

Updated at

2022-09-11 09:32:26 UTC

NP-MRD ID

NP0312608

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl (2r,3s)-3-nonyloxirane-2-carboxylate

Description

(2R,3S)-3-Nonyloxirane-2-carboxylic acid methyl ester belongs to the class of organic compounds known as oxirane carboxylic acids. Oxirane carboxylic acids are compounds containing an oxirane ring bearing a carboxylic acid group. methyl (2r,3s)-3-nonyloxirane-2-carboxylate is found in Gracilaria gracilis. Based on a literature review very few articles have been published on (2R,3S)-3-Nonyloxirane-2-carboxylic acid methyl ester.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 40  0  0  0  0  0  0  0  0999 V2000
   -5.8220    2.0856   -0.5787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4030    0.6320   -0.6610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9908    0.5482   -0.1506 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4594   -0.8797   -0.1869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0321   -0.7873    0.3579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3582   -2.1133    0.3912 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0317   -1.9452    0.9493 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8784   -1.0195    0.1290 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2404   -0.9645    0.8073 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1644   -0.0441    0.0373 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4230   -0.3890   -1.2983 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4538   -0.6015   -0.3841 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6082    0.3302   -0.3671 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7941   -0.0269   -0.1727 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3745    1.6820   -0.5778 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4277    2.6381   -0.5766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9227    2.2035   -0.5309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3080    2.5301    0.2916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3914    2.5902   -1.4899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4666    0.3415   -1.7373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1253    0.0531   -0.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3597    1.1958   -0.7566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9950    0.9042    0.8999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3980   -1.2525   -1.2296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0713   -1.5603    0.4173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5007   -0.1496   -0.4018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0787   -0.3319    1.3488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9278   -2.8888    0.9395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2261   -2.5143   -0.6447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0448   -1.5056    1.9880 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5358   -2.9225    1.1046 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9544   -1.3681   -0.9020 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4265    0.0078    0.1107 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6333   -1.9971    0.8221 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0618   -0.5429    1.8155 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0846    1.0403    0.2274 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7133   -1.6647   -0.2091 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4901    3.0405    0.4747 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1806    3.4720   -1.2577 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4047    2.1741   -0.8325 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
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 12 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  0
  4 25  1  0
  5 26  1  0
  5 27  1  0
  6 28  1  0
  6 29  1  0
  7 30  1  0
  7 31  1  0
  8 32  1  0
  8 33  1  0
  9 34  1  0
  9 35  1  0
 10 36  1  6
 12 37  1  1
 16 38  1  0
 16 39  1  0
 16 40  1  0
M  END


  Mrv1652309112211322D          

 16 16  0  0  1  0            999 V2000
    3.8230   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5375   -1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2520   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9664   -1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6809   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3954   -1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1099   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8243   -1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5388   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2533   -1.3184    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.6658   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0783   -1.3184    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.7927   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5072   -1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7927   -2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5072   -2.9684    0.0000 C   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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  1  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0312608

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCCC[C@@H]1O[C@H]1C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C13H24O3/c1-3-4-5-6-7-8-9-10-11-12(16-11)13(14)15-2/h11-12H,3-10H2,1-2H3/t11-,12+/m0/s1

> <INCHI_KEY>
MPTQVTVEEUZMMR-NWDGAFQWSA-N

> <FORMULA>
C13H24O3

> <MOLECULAR_WEIGHT>
228.332

> <EXACT_MASS>
228.172544633

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
27.794501989276206

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (2R,3S)-3-nonyloxirane-2-carboxylate

> <JCHEM_LOGP>
3.8399362183333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.277033476968083

> <JCHEM_POLAR_SURFACE_AREA>
38.83

> <JCHEM_REFRACTIVITY>
62.79230000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (2R,3S)-3-nonyloxirane-2-carboxylate

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0       7.136  -3.231   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.470  -2.461   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.804  -3.231   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.137  -2.461   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.471  -3.231   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.805  -2.461   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      15.138  -3.231   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      16.472  -2.461   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      17.806  -3.231   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      19.139  -2.461   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      19.909  -1.127   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      20.679  -2.461   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      22.013  -3.231   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      23.347  -2.461   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      22.013  -4.771   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      23.347  -5.541   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10   12                                                       
CONECT   12   11   10   13                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Value	Source
(2R,3S)-3-Nonyloxirane-2-carboxylate methyl ester	Generator

Chemical Formula

C₁₃H₂₄O₃

Average Mass

228.3320 Da

Monoisotopic Mass

228.17254 Da

IUPAC Name

methyl (2R,3S)-3-nonyloxirane-2-carboxylate

Traditional Name

methyl (2R,3S)-3-nonyloxirane-2-carboxylate

CAS Registry Number

Not Available

SMILES

CCCCCCCCC[C@@H]1O[C@H]1C(=O)OC

InChI Identifier

InChI=1S/C13H24O3/c1-3-4-5-6-7-8-9-10-11-12(16-11)13(14)15-2/h11-12H,3-10H2,1-2H3/t11-,12+/m0/s1

InChI Key

MPTQVTVEEUZMMR-NWDGAFQWSA-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
Gracilaria gracilis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxirane carboxylic acids. Oxirane carboxylic acids are compounds containing an oxirane ring bearing a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Epoxides

Sub Class

Oxirane carboxylic acids and derivatives

Direct Parent

Oxirane carboxylic acids

Alternative Parents

Substituents

Oxirane carboxylic acid
Methyl ester
Carboxylic acid ester
Oxacycle
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
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	3.84	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	38.83 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	62.79 m³·mol⁻¹	ChemAxon
Polarizability	27.79 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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

9064934

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10889670

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for methyl (2r,3s)-3-nonyloxirane-2-carboxylate (NP0312608)

MOL for NP0312608 (methyl (2r,3s)-3-nonyloxirane-2-carboxylate)

3D MOL for NP0312608 (methyl (2r,3s)-3-nonyloxirane-2-carboxylate)

3D SDF for NP0312608 (methyl (2r,3s)-3-nonyloxirane-2-carboxylate)

3D-SDF for NP0312608 (methyl (2r,3s)-3-nonyloxirane-2-carboxylate)

PDB for NP0312608 (methyl (2r,3s)-3-nonyloxirane-2-carboxylate)

3D PDB for NP0312608 (methyl (2r,3s)-3-nonyloxirane-2-carboxylate)

SMILES for NP0312608 (methyl (2r,3s)-3-nonyloxirane-2-carboxylate)

INCHI for NP0312608 (methyl (2r,3s)-3-nonyloxirane-2-carboxylate)

Structure for NP0312608 (methyl (2r,3s)-3-nonyloxirane-2-carboxylate)

3D Structure for NP0312608 (methyl (2r,3s)-3-nonyloxirane-2-carboxylate)