Hmdb loader

Showing metabocard for 3-Oxo-1,8-octanedicarboxylic acid (HMDB0341260)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:01:41 UTC
Update Date2022-09-22 18:34:44 UTC
HMDB IDHMDB0341260
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Oxo-1,8-octanedicarboxylic acid
Description4-Oxosebacic Acid, also known as 4-oxosebacate, belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain. 4-Oxosebacic Acid is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for HMDB0341260 (3-Oxo-1,8-octanedicarboxylic acid)

4OX
  Mrv0541 02231216052D          

 15 14  0  0  0  0            999 V2000
   -1.0704   -0.1530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7848    0.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4993   -0.1530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2138    0.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9282   -0.1530    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2138    1.0845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9309    0.2595    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2165   -0.1530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2165   -0.9780    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5020    0.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7875   -0.1530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0731    0.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3586   -0.1530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3559    0.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0731    1.0845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 14  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
  4  6  2  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 15  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
Download

3D MOL for HMDB0341260 (3-Oxo-1,8-octanedicarboxylic acid)

Download
3D SDF for HMDB0341260 (3-Oxo-1,8-octanedicarboxylic acid)
4OX
  Mrv0541 02231216052D          

 15 14  0  0  0  0            999 V2000
   -1.0704   -0.1530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7848    0.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4993   -0.1530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2138    0.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9282   -0.1530    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2138    1.0845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9309    0.2595    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2165   -0.1530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2165   -0.9780    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5020    0.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7875   -0.1530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0731    0.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3586   -0.1530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3559    0.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0731    1.0845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 14  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
  4  6  2  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 15  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341260

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H16O5/c11-8(6-7-10(14)15)4-2-1-3-5-9(12)13/h1-7H2,(H,12,13)(H,14,15)

> <INCHI_KEY>
XTQIBFVBYWIHIP-UHFFFAOYSA-N

> <FORMULA>
C10H16O5

> <MOLECULAR_WEIGHT>
216.231

> <EXACT_MASS>
216.099773622

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
22.5148624475965

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-oxodecanedioic acid

> <ALOGPS_LOGP>
0.51

> <JCHEM_LOGP>
1.0897112973333334

> <ALOGPS_LOGS>
-1.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.909826477257549

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.3077458261688895

> <JCHEM_PKA_STRONGEST_BASIC>
-7.356576829685785

> <JCHEM_POLAR_SURFACE_AREA>
91.66999999999999

> <JCHEM_REFRACTIVITY>
51.784400000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.23e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
sebacic acids

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for HMDB0341260 (3-Oxo-1,8-octanedicarboxylic acid)
Download
PDB for HMDB0341260 (3-Oxo-1,8-octanedicarboxylic acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 4OX                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -1.998  -0.286   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.332   0.484   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.665  -0.286   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.999   0.484   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -7.333  -0.286   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -5.999   2.024   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       7.338   0.484   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.004  -0.286   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.004  -1.826   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.670   0.484   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.337  -0.286   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.003   0.484   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.669  -0.286   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.664   0.484   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.003   2.024   0.000  0.00  0.00           O+0
CONECT    1    2   14                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    8                                                            
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14    1   13                                                       
CONECT   15   12                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

Download
3D PDB for HMDB0341260 (3-Oxo-1,8-octanedicarboxylic acid)
Download
SMILES for HMDB0341260 (3-Oxo-1,8-octanedicarboxylic acid)
OC(=O)CCCCCC(=O)CCC(O)=O
Download
INCHI for HMDB0341260 (3-Oxo-1,8-octanedicarboxylic acid)
InChI=1S/C10H16O5/c11-8(6-7-10(14)15)4-2-1-3-5-9(12)13/h1-7H2,(H,12,13)(H,14,15)
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
4-OxosebacateGenerator
4-OxodecanedioateGenerator
Chemical FormulaC10H16O5
Average Molecular Weight216.231
Monoisotopic Molecular Weight216.099773622
IUPAC Name4-oxodecanedioic acid
Traditional Namesebacic acids
CAS Registry NumberNot Available
SMILES
OC(=O)CCCCCC(=O)CCC(O)=O
InChI Identifier
InChI=1S/C10H16O5/c11-8(6-7-10(14)15)4-2-1-3-5-9(12)13/h1-7H2,(H,12,13)(H,14,15)
InChI KeyXTQIBFVBYWIHIP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12  carbon atoms long side chain.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassKeto acids and derivatives  
Sub ClassMedium-chain keto acids and derivatives  
Direct ParentMedium-chain keto acids and derivatives  
Alternative Parents
Substituents
  • Medium-chain keto acid
    • 

  • Gamma-keto acid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Ketone
    • 

  • 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
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Predicted Kovats Retention Indices
Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB02260  
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound1755  
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920  ]