Showing NP-Card for methyl (2z)-7-[(2s,3r)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate (NP0309377)

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Record Information
Version2.0
Created at2022-09-11 03:56:30 UTC
Updated at2022-09-11 03:56:30 UTC
NP-MRD IDNP0309377
Secondary Accession NumbersNone
Natural Product Identification
Common Namemethyl (2z)-7-[(2s,3r)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate
DescriptionMethyl 8s,9r-epoxy-2z-decen-4,6-diynoate belongs to the class of organic compounds known as fatty acid esters. These are carboxylic ester derivatives of a fatty acid. methyl (2z)-7-[(2s,3r)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate is found in Chrysoma pauciflosculosa and Erigeron philadelphicus. Based on a literature review very few articles have been published on Methyl 8s,9r-epoxy-2z-decen-4,6-diynoate.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0309377 (methyl (2z)-7-[(2s,3r)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate)

  Mrv1652309112205562D          

 14 14  0  0  1  0            999 V2000
    3.0960    5.0138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3816    5.4263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6671    5.0138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6671    4.1888    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    5.4263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    5.0138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    4.1888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    3.3638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    2.5388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    1.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6507    0.1743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8888   -0.2382    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  3  0  0  0  0
  8  9  1  0  0  0  0
  9 10  3  0  0  0  0
 11 10  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
M  END
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3D MOL for NP0309377 (methyl (2z)-7-[(2s,3r)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate)

     RDKit          3D

 24 24  0  0  0  0  0  0  0  0999 V2000
    4.4006    1.9411    0.3954 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4469    0.7085   -0.2583 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3245   -0.0999   -0.3781 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2714    0.3192    0.1223 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4814   -1.3627   -1.0772 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4246   -2.1372   -1.1969 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1849   -1.6965   -0.6353 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -1.3391   -0.1613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1287   -0.9337    0.3908 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1859   -0.6003    0.8707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4764   -0.2199    1.4565 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.5947   -1.0368    0.8608 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4645    0.3930    0.6817 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2846    0.7742   -0.7488 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4431    2.2842    0.5891 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8681    1.9008    1.3464 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9451    2.7333   -0.2628 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4528   -1.6709   -1.4980 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4900   -3.1000   -1.7155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5959   -0.3243    2.5639 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3527    0.8836    1.1741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2116    0.7142   -1.0482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8677    0.0542   -1.3765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6812    1.8150   -0.9003 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  2  0
  6  7  1  0
  7  8  3  0
  8  9  1  0
  9 10  3  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 11  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  5 18  1  0
  6 19  1  0
 11 20  1  1
 13 21  1  1
 14 22  1  0
 14 23  1  0
 14 24  1  0
M  END
Download

3D SDF for NP0309377 (methyl (2z)-7-[(2s,3r)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate)

  Mrv1652309112205562D          

 14 14  0  0  1  0            999 V2000
    3.0960    5.0138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3816    5.4263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6671    5.0138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6671    4.1888    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    5.4263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    5.0138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    4.1888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    3.3638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    2.5388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    1.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6507    0.1743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8888   -0.2382    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  3  0  0  0  0
  8  9  1  0  0  0  0
  9 10  3  0  0  0  0
 11 10  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0309377

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)\C=C/C#CC#C[C@@H]1O[C@@H]1C

> <INCHI_IDENTIFIER>
InChI=1S/C11H10O3/c1-9-10(14-9)7-5-3-4-6-8-11(12)13-2/h6,8-10H,1-2H3/b8-6-/t9-,10+/m1/s1

> <INCHI_KEY>
PCDNXYJKUQSRGB-VCNAMUQVSA-N

> <FORMULA>
C11H10O3

> <MOLECULAR_WEIGHT>
190.198

> <EXACT_MASS>
190.062994182

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
19.60384046706126

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (2Z)-7-[(2S,3R)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate

> <JCHEM_LOGP>
1.9136701643333325

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.989451729080322

> <JCHEM_PKA_STRONGEST_BASIC>
-4.292619755615399

> <JCHEM_POLAR_SURFACE_AREA>
38.83

> <JCHEM_REFRACTIVITY>
53.50670000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (2Z)-7-[(2S,3R)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for NP0309377 (methyl (2z)-7-[(2s,3r)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate)

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PDB for NP0309377 (methyl (2z)-7-[(2s,3r)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate)
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       5.779   9.359   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       4.446  10.129   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       3.112   9.359   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.112   7.819   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.778  10.129   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.445   9.359   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.445   7.819   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.445   6.279   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.445   4.739   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.445   3.199   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.445   1.659   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.215   0.325   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.325   0.325   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.659  -0.445   0.000  0.00  0.00           C+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                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11   13                                                       
CONECT   13   12   11   14                                                  
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

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3D PDB for NP0309377 (methyl (2z)-7-[(2s,3r)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate)
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SMILES for NP0309377 (methyl (2z)-7-[(2s,3r)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate)
COC(=O)\C=C/C#CC#C[C@@H]1O[C@@H]1C
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INCHI for NP0309377 (methyl (2z)-7-[(2s,3r)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate)
InChI=1S/C11H10O3/c1-9-10(14-9)7-5-3-4-6-8-11(12)13-2/h6,8-10H,1-2H3/b8-6-/t9-,10+/m1/s1
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View in JSmol
Synonyms
ValueSource
Methyl 8S,9R-epoxy-2Z-decen-4,6-diynoic acidGenerator
Chemical FormulaC11H10O3
Average Mass190.1980 Da
Monoisotopic Mass190.06299 Da
IUPAC Namemethyl (2Z)-7-[(2S,3R)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate
Traditional Namemethyl (2Z)-7-[(2S,3R)-3-methyloxiran-2-yl]hept-2-en-4,6-diynoate
CAS Registry NumberNot Available
SMILES
COC(=O)\C=C/C#CC#C[C@@H]1O[C@@H]1C
InChI Identifier
InChI=1S/C11H10O3/c1-9-10(14-9)7-5-3-4-6-8-11(12)13-2/h6,8-10H,1-2H3/b8-6-/t9-,10+/m1/s1
InChI KeyPCDNXYJKUQSRGB-VCNAMUQVSA-N
Experimental Spectra
Not Available
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Chrysoma pauciflosculosaLOTUS Database
Erigeron philadelphicusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as fatty acid esters. These are carboxylic ester derivatives of a fatty acid.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassFatty Acyls  
Sub ClassFatty acid esters  
Direct ParentFatty acid esters  
Alternative Parents
Substituents
  • Fatty acid ester
    • 

  • Methyl ester
    • 

  • Enoate ester
    • 

  • Alpha,beta-unsaturated carboxylic ester
    • 

  • Carboxylic acid ester
    • 

  • Carboxylic acid derivative
    • 

  • Dialkyl ether
    • 

  • Oxirane
    • 

  • Ether
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Organooxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP1.91ChemAxon
pKa (Strongest Acidic)18.99ChemAxon
pKa (Strongest Basic)-4.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area38.83 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity53.51 m³·mol⁻¹ChemAxon
Polarizability19.6 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID113369128  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound101633876  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]