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Showing NP-Card for cis-5-Decenedioic acid (NP0339225)

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Record Information
Version2.0
Created at2024-09-11 20:31:58 UTC
Updated at2024-09-11 20:31:59 UTC
NP-MRD IDNP0339225
Secondary Accession NumbersNone
Natural Product Identification
Common Namecis-5-Decenedioic acid
DescriptionCis-5-Decenedioic acid, also known as cis-5-decene -1,10-dioate, 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. Cis-5-Decenedioic acid is a weakly acidic compound (based on its pKa). cis-5-Decenedioic acid was first documented in 1990 (PMID: 2380628). Cis-5-Decenedioic acid, with regard to humans, has been linked to the inborn metabolic disorder medium chain acyl-coa dehydrogenase deficiency.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0339225 (cis-5-Decenedioic acid)


  Mrv0541 02251208192D          

 14 13  0  0  0  0            999 V2000
   10.1751   -2.5377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8896   -2.9502    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8896   -3.7752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6041   -4.1878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6041   -5.0128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1751   -1.7127    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4606   -2.9502    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.3185   -5.4253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0330   -5.0128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4619   -5.0128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1765   -5.4253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1765   -6.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.8909   -5.0128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.7475   -5.4253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  7  1  2  0  0  0  0
  8  5  2  0  0  0  0
  9  8  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 13 11  2  0  0  0  0
 14 10  1  0  0  0  0
  9 14  1  0  0  0  0
M  END
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3D MOL for NP0339225 (cis-5-Decenedioic acid)

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3D SDF for NP0339225 (cis-5-Decenedioic acid)

  Mrv0541 02251208192D          

 14 13  0  0  0  0            999 V2000
   10.1751   -2.5377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8896   -2.9502    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8896   -3.7752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6041   -4.1878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6041   -5.0128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1751   -1.7127    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4606   -2.9502    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.3185   -5.4253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0330   -5.0128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4619   -5.0128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1765   -5.4253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1765   -6.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.8909   -5.0128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.7475   -5.4253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  7  1  2  0  0  0  0
  8  5  2  0  0  0  0
  9  8  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 13 11  2  0  0  0  0
 14 10  1  0  0  0  0
  9 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0339225

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CCC\C=C/CCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H16O4/c11-9(12)7-5-3-1-2-4-6-8-10(13)14/h1-2H,3-8H2,(H,11,12)(H,13,14)/b2-1-

> <INCHI_KEY>
WAGQZQAZCIOEDU-UPHRSURJSA-N

> <FORMULA>
C10H16O4

> <MOLECULAR_WEIGHT>
200.2316

> <EXACT_MASS>
200.104859

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
21.392409550497508

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5Z)-dec-5-enedioic acid

> <ALOGPS_LOGP>
1.79

> <JCHEM_LOGP>
1.9070073659999993

> <ALOGPS_LOGS>
-2.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.256174785049645

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.654114793721683

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
52.259600000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.40e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5Z)-dec-5-enedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0339225 (cis-5-Decenedioic acid)
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PDB for NP0339225 (cis-5-Decenedioic acid)
HEADER    PROTEIN                                 25-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-FEB-12         0                                  
HETATM    1  C   UNK     0      18.994  -4.737   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      20.327  -5.507   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      20.327  -7.047   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      21.661  -7.817   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      21.661  -9.357   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      18.994  -3.197   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      17.660  -5.507   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      22.995 -10.127   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      24.328  -9.357   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      26.996  -9.357   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      28.329 -10.127   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      28.329 -11.667   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      29.663  -9.357   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      25.662 -10.127   0.000  0.00  0.00           C+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    8                                                       
CONECT    6    1                                                            
CONECT    7    1                                                            
CONECT    8    5    9                                                       
CONECT    9    8   14                                                       
CONECT   10   11   14                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   10    9                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

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3D PDB for NP0339225 (cis-5-Decenedioic acid)
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SMILES for NP0339225 (cis-5-Decenedioic acid)
OC(=O)CCC\C=C/CCCC(O)=O
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INCHI for NP0339225 (cis-5-Decenedioic acid)
InChI=1S/C10H16O4/c11-9(12)7-5-3-1-2-4-6-8-10(13)14/h1-2H,3-8H2,(H,11,12)(H,13,14)/b2-1-
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Synonyms
ValueSource
cis-5-DecenedioateGenerator
cis-5-Decene -1,10-dioateHMDB
cis-5-Decene -1,10-dioic acidHMDB
cis-5-Decene-1,10-dioiateHMDB
cis-5-DecenedioiateHMDB
(5Z)-Dec-5-enedioateGenerator
Chemical FormulaC10H16O4
Average Mass200.2316 Da
Monoisotopic Mass200.10486 Da
IUPAC Name(5Z)-dec-5-enedioic acid
Traditional Name(5Z)-dec-5-enedioic acid
CAS Registry NumberNot Available
SMILES
OC(=O)CCC\C=C/CCCC(O)=O
InChI Identifier
InChI=1S/C10H16O4/c11-9(12)7-5-3-1-2-4-6-8-10(13)14/h1-2H,3-8H2,(H,11,12)(H,13,14)/b2-1-
InChI KeyWAGQZQAZCIOEDU-UPHRSURJSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
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.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassFatty Acyls  
Sub ClassFatty acids and conjugates  
Direct ParentMedium-chain fatty acids  
Alternative Parents
Substituents
  • Medium-chain 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 FrameworkAliphatic acyclic 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
logP1.79ALOGPS
logP1.91ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)4.65ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity52.26 m³·mol⁻¹ChemAxon
Polarizability21.39 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0013227  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB029345  
KNApSAcK IDNot Available
Chemspider ID5880465  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound7563148  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Tserng KY, Jin SJ, Kerr DS, Hoppel CL: Abnormal urinary excretion of unsaturated dicarboxylic acids in patients with medium-chain acyl-CoA dehydrogenase deficiency. J Lipid Res. 1990 May;31(5):763-71. [PubMed:2380628  ]