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Showing NP-Card for Dimethyl succinate (NP0001264)

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Record Information
Version2.0
Created at2012-09-11 18:36:40 UTC
Updated at2024-09-03 04:22:57 UTC
NP-MRD IDNP0001264
Natural Product DOIhttps://doi.org/10.57994/3045
Secondary Accession NumbersNone
Natural Product Identification
Common NameDimethyl succinate
DescriptionDimethyl succinate, also known as DBE-4 or fema 2396, belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0001264 (Dimethyl succinate)


  Mrv1652305271900092D          

 10  9  0  0  0  0            999 V2000
    4.3974    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  2  0  0  0  0
  8  6  2  0  0  0  0
  9  1  1  0  0  0  0
  9  5  1  0  0  0  0
 10  2  1  0  0  0  0
 10  6  1  0  0  0  0
M  END
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3D MOL for NP0001264 (Dimethyl succinate)

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3D SDF for NP0001264 (Dimethyl succinate)

  Mrv1652305271900092D          

 10  9  0  0  0  0            999 V2000
    4.3974    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  2  0  0  0  0
  8  6  2  0  0  0  0
  9  1  1  0  0  0  0
  9  5  1  0  0  0  0
 10  2  1  0  0  0  0
 10  6  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001264

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)CCC(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O4/c1-9-5(7)3-4-6(8)10-2/h3-4H2,1-2H3

> <INCHI_KEY>
MUXOBHXGJLMRAB-UHFFFAOYSA-N

> <FORMULA>
C6H10O4

> <MOLECULAR_WEIGHT>
146.1412

> <EXACT_MASS>
146.057908808

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
14.27175470097833

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,4-dimethyl butanedioate

> <ALOGPS_LOGP>
0.20

> <JCHEM_LOGP>
-0.10669485533333355

> <ALOGPS_LOGS>
-0.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.728716400162713

> <JCHEM_POLAR_SURFACE_AREA>
52.60000000000001

> <JCHEM_REFRACTIVITY>
33.0752

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.70e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dimethyl succinate

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0001264 (Dimethyl succinate)
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PDB for NP0001264 (Dimethyl succinate)
HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       8.208   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.127   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.207   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.541   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       5.541   2.310   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.540  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       6.875   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.206   0.770   0.000  0.00  0.00           O+0
CONECT    1    9                                                            
CONECT    2   10                                                            
CONECT    3    4    5                                                       
CONECT    4    3    6                                                       
CONECT    5    3    7    9                                                  
CONECT    6    4    8   10                                                  
CONECT    7    5                                                            
CONECT    8    6                                                            
CONECT    9    1    5                                                       
CONECT   10    2    6                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0001264 (Dimethyl succinate)
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SMILES for NP0001264 (Dimethyl succinate)
COC(=O)CCC(=O)OC
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INCHI for NP0001264 (Dimethyl succinate)
InChI=1S/C6H10O4/c1-9-5(7)3-4-6(8)10-2/h3-4H2,1-2H3
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Synonyms
ValueSource
Dimethyl succinic acidGenerator
Butanedioic acid, 1,4-dimethyl esterHMDB
Butanedioic acid, dimethyl esterHMDB
CH3OC(O)CH2CH2C(O)OCH3HMDB
DBE-4HMDB
DBE-4 dibasic esterHMDB
Dimethyl ester OF succinic acidHMDB
DimethylsuccinateHMDB
FEMA 2396HMDB
Methyl butanedioateHMDB
Methyl succinateHMDB
Succinic acid dimethyl esterHMDB
Succinic acid, dimethyl esterHMDB
1,4-Dimethyl butanedioic acidGenerator
Dimethyl succinateMeSH
Chemical FormulaC6H10O4
Average Mass146.1412 Da
Monoisotopic Mass146.05791 Da
IUPAC Name1,4-dimethyl butanedioate
Traditional Namedimethyl succinate
CAS Registry Number106-65-0
SMILES
COC(=O)CCC(=O)OC
InChI Identifier
InChI=1S/C6H10O4/c1-9-5(7)3-4-6(8)10-2/h3-4H2,1-2H3
InChI KeyMUXOBHXGJLMRAB-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
HSQC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-07-05View Spectrum
COSY NMR[1H, 1H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-07-05View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-07-05View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-07-05View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-07-05View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, CDCl3, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 25.16 MHz, CDCl3, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600, CD3OD, simulated)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-07-05View Spectrum
Species
Species of Origin
Species NameSourceReference
Astragalus membranaceus
Chemical Taxonomy
Description Belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassFatty Acyls  
Sub ClassFatty acid esters  
Direct ParentFatty acid methyl esters  
Alternative Parents
Substituents
  • Fatty acid methyl ester
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Methyl ester
    • 

  • Carboxylic acid ester
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateLiquid
Experimental Properties
PropertyValueReference
Melting Point19 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP0.35Not Available
Predicted Properties
PropertyValueSource
Water Solubility67 g/LALOGPS
logP0.2ALOGPS
logP-0.11ChemAxon
logS-0.34ALOGPS
pKa (Strongest Basic)-6.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area52.6 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity33.08 m³·mol⁻¹ChemAxon
Polarizability14.27 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0033837  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012011  
KNApSAcK IDNot Available
Chemspider ID13848341  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound7820  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1.  (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. . 
  2. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.