NP-MRD: Showing NP-Card for 3,4-methylenesebacic acid (NP0289467)

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Record Information

Version

2.0

Created at

2022-09-09 19:40:06 UTC

Updated at

2022-09-09 19:40:06 UTC

NP-MRD ID

NP0289467

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3,4-methylenesebacic acid

Description

3,4-Methylenesebacic acid belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. 3,4-Methylenesebacic acid is a weakly acidic compound (based on its pKa). 3,4-methylenesebacic acid is found in Arabidopsis thaliana. These are fatty acids containing a branched chain.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 33  0  0  0  0  0  0  0  0999 V2000
   -0.5759    1.4271   -0.6153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9386    0.6538    0.3890 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0202    0.2118    1.4270 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4301    0.2161    1.1940 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9728   -0.8091    0.2561 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4689   -0.8361   -1.1346 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1926   -1.9759   -1.8770 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6569   -1.7825   -1.9025 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3547   -2.2455   -0.9674 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2871   -1.1071   -2.9242 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3459    0.2411    0.4504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8471   -0.5317    1.3934 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3227    0.6937   -0.5985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5249    2.1397   -0.5928 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2416    2.6839   -1.4660 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9390    2.9472    0.3673 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4396    1.8045   -0.7543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2561    1.7511   -1.4000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3126    0.7737    2.3585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3018   -0.8663    1.7167 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8272    1.2437    0.9518 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9071   -0.0076    2.2077 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1083   -0.6778    0.1554 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9068   -1.8486    0.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3852   -1.0811   -1.1098 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7132    0.0921   -1.6566 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8229   -1.9864   -2.9156 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8814   -2.9287   -1.4103 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9507   -0.3471   -2.7811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8796   -0.8346    1.4377 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2125   -0.8907    2.1769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8033    0.4396   -1.5710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2559    0.1090   -0.5005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5278    3.3286    1.1007 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  8  1  0
  8  9  2  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  3
  2 11  1  0
 11 12  2  3
 11 13  1  0
 13 14  1  0
 14 16  1  0
 14 15  2  0
 10 29  1  0
  7 27  1  0
  7 28  1  0
  6 25  1  0
  6 26  1  0
  5 23  1  0
  5 24  1  0
  4 21  1  0
  4 22  1  0
  3 19  1  0
  3 20  1  0
  1 17  1  0
  1 18  1  0
 12 30  1  0
 12 31  1  0
 13 32  1  0
 13 33  1  0
 16 34  1  0
M  END


  Mrv0541 02261312002D          

 16 15  0  0  0  0            999 V2000
    3.5211    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355    4.0954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6645    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3789    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0934    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8079    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5224    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5224    4.0954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2368    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2368    2.0329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9513    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6658    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3802    3.2704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6658    2.0329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  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
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0289467

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CCCCCC(=C)C(=C)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H18O4/c1-9(10(2)8-12(15)16)6-4-3-5-7-11(13)14/h1-8H2,(H,13,14)(H,15,16)

> <INCHI_KEY>
YVOCTABTPCVYNG-UHFFFAOYSA-N

> <FORMULA>
C12H18O4

> <MOLECULAR_WEIGHT>
226.2689

> <EXACT_MASS>
226.120509064

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
24.362427658591564

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3,4-dimethylidenedecanedioic acid

> <ALOGPS_LOGP>
2.08

> <JCHEM_LOGP>
2.147675593333333

> <ALOGPS_LOGS>
-2.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.2615983807684765

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.656979125707469

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
59.795199999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.61e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,4-dimethylidenedecanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-FEB-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-FEB-13         0                                  
HETATM    1  O   UNK     0       6.573   5.335   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       7.906   6.105   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       7.906   7.645   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       9.240   5.335   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.574   6.105   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.907   5.335   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      13.241   6.105   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      14.575   5.335   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      15.908   6.105   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      15.908   7.645   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      17.242   5.335   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      17.242   3.795   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      18.576   6.105   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      19.909   5.335   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      21.243   6.105   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      19.909   3.795   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

View in JSmol

Synonyms

Value	Source
3,4-Methylenesebacate	Generator
3,4-Dimethylidenedecanedioate	Generator

Chemical Formula

C₁₂H₁₈O₄

Average Mass

226.2689 Da

Monoisotopic Mass

226.12051 Da

IUPAC Name

3,4-dimethylidenedecanedioic acid

Traditional Name

3,4-dimethylidenedecanedioic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CCCCCC(=C)C(=C)CC(O)=O

InChI Identifier

InChI=1S/C12H18O4/c1-9(10(2)8-12(15)16)6-4-3-5-7-11(13)14/h1-8H2,(H,13,14)(H,15,16)

InChI Key

YVOCTABTPCVYNG-UHFFFAOYSA-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
Arabidopsis thaliana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Medium-chain fatty acids

Alternative Parents

Substituents

Medium-chain fatty acid
Branched fatty acid
Unsaturated fatty acid
Dicarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic 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	2.08	ALOGPS
logP	2.15	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	4.66	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	59.8 m³·mol⁻¹	ChemAxon
Polarizability	24.36 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0059729

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

124202122

PDB ID

Not Available

ChEBI ID

89935

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3,4-methylenesebacic acid (NP0289467)

MOL for NP0289467 (3,4-methylenesebacic acid)

3D MOL for NP0289467 (3,4-methylenesebacic acid)

3D SDF for NP0289467 (3,4-methylenesebacic acid)

3D-SDF for NP0289467 (3,4-methylenesebacic acid)

PDB for NP0289467 (3,4-methylenesebacic acid)

3D PDB for NP0289467 (3,4-methylenesebacic acid)

SMILES for NP0289467 (3,4-methylenesebacic acid)

INCHI for NP0289467 (3,4-methylenesebacic acid)

Structure for NP0289467 (3,4-methylenesebacic acid)

3D Structure for NP0289467 (3,4-methylenesebacic acid)