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Showing NP-Card for 3-Oxoadipic acid (NP0001317)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-19 23:59:01 UTC
NP-MRD IDNP0001317
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Oxoadipic acid
Description3-Oxoadipic acid is a regularly occurring Adipic dicarboxylic acid human metabolite found occasionally in biofluids of healthy individuals. (PMIDs 8340451, 1769109, 2338430) Increased amounts of 3-Oxoadipic acid are excreted after ingestion of Sebacic acid, supporting the hypothesis that dicarboxylic acids are degraded by ordinary beta-oxidation. (PMID 3220884 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001317 (3-Oxoadipic acid)


  Mrv1652305261923582D          

 11 10  0  0  0  0            999 V2000
   -0.3265   -0.1138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3911    0.2999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0403    0.2999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3265   -0.9378    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1049   -0.1138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7540   -0.1138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8186    0.2999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4679    0.3038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7540   -0.9378    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5324   -0.1138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8186    1.1276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  2  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
  7 10  1  0  0  0  0
  7 11  2  0  0  0  0
M  END
Download

3D MOL for NP0001317 (3-Oxoadipic acid)

HMDB0000398
     RDKit          3D
3-Oxoadipic acid
 19 18  0  0  0  0  0  0  0  0999 V2000
   -3.0018    1.1745   -0.3924 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4173    0.6084    0.5726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1143    1.3353    1.7096 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0409   -0.8291    0.5233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8233   -1.0351   -0.3608 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3471   -0.2893    0.1200 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2785    0.3865    1.1222 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -0.3950   -0.6671 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6996    0.4048   -0.0639 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3806   -0.0944    0.8630 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9764    1.6888   -0.5025 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6752    2.2488    1.6763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9051   -1.2125    1.5460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9142   -1.3589    0.0785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5936   -2.1307   -0.3354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1041   -0.7944   -1.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8936   -1.4899   -0.6078 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4457   -0.1623   -1.7422 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9563    1.9444   -0.6110 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  8 17  1  0
  8 18  1  0
 11 19  1  0
M  END
Download

3D SDF for NP0001317 (3-Oxoadipic acid)


  Mrv1652305261923582D          

 11 10  0  0  0  0            999 V2000
   -0.3265   -0.1138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3911    0.2999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0403    0.2999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3265   -0.9378    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1049   -0.1138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7540   -0.1138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8186    0.2999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4679    0.3038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7540   -0.9378    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5324   -0.1138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8186    1.1276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  2  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
  7 10  1  0  0  0  0
  7 11  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0001317

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O5/c7-4(3-6(10)11)1-2-5(8)9/h1-3H2,(H,8,9)(H,10,11)

> <INCHI_KEY>
RTGHRDFWYQHVFW-UHFFFAOYSA-N

> <FORMULA>
C6H8O5

> <MOLECULAR_WEIGHT>
160.1247

> <EXACT_MASS>
160.037173366

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
13.910695418944067

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-oxohexanedioic acid

> <ALOGPS_LOGP>
-0.64

> <JCHEM_LOGP>
-0.1766289986666666

> <ALOGPS_LOGS>
-0.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.235829200342627

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4748505038613793

> <JCHEM_PKA_STRONGEST_BASIC>
-7.5471659957939785

> <JCHEM_POLAR_SURFACE_AREA>
91.66999999999999

> <JCHEM_REFRACTIVITY>
33.4322

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.71e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-oxoadipic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001317 (3-Oxoadipic acid)

HMDB0000398
     RDKit          3D
3-Oxoadipic acid
 19 18  0  0  0  0  0  0  0  0999 V2000
   -3.0018    1.1745   -0.3924 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4173    0.6084    0.5726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1143    1.3353    1.7096 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0409   -0.8291    0.5233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8233   -1.0351   -0.3608 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3471   -0.2893    0.1200 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2785    0.3865    1.1222 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -0.3950   -0.6671 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6996    0.4048   -0.0639 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3806   -0.0944    0.8630 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9764    1.6888   -0.5025 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6752    2.2488    1.6763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9051   -1.2125    1.5460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9142   -1.3589    0.0785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5936   -2.1307   -0.3354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1041   -0.7944   -1.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8936   -1.4899   -0.6078 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4457   -0.1623   -1.7422 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9563    1.9444   -0.6110 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  8 17  1  0
  8 18  1  0
 11 19  1  0
M  END
Download

PDB for NP0001317 (3-Oxoadipic acid)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0      -0.609  -0.212   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.730   0.560   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.942   0.560   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.609  -1.751   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.062  -0.212   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.274  -0.212   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.395   0.560   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -4.607   0.567   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -3.274  -1.751   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.727  -0.212   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.395   2.105   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1                                                            
CONECT    5    2    7                                                       
CONECT    6    3    8    9                                                  
CONECT    7    5   10   11                                                  
CONECT    8    6                                                            
CONECT    9    6                                                            
CONECT   10    7                                                            
CONECT   11    7                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for NP0001317 (3-Oxoadipic acid)

COMPND    HMDB0000398
HETATM    1  O1  UNL     1      -3.002   1.174  -0.392  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.417   0.608   0.573  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.114   1.335   1.710  1.00  0.00           O  
HETATM    4  C2  UNL     1      -2.041  -0.829   0.523  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.823  -1.035  -0.361  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.347  -0.289   0.120  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.279   0.386   1.122  1.00  0.00           O  
HETATM    8  C5  UNL     1       1.612  -0.395  -0.667  1.00  0.00           C  
HETATM    9  C6  UNL     1       2.700   0.405  -0.064  1.00  0.00           C  
HETATM   10  O4  UNL     1       3.381  -0.094   0.863  1.00  0.00           O  
HETATM   11  O5  UNL     1       2.976   1.689  -0.503  1.00  0.00           O  
HETATM   12  H1  UNL     1      -1.675   2.249   1.676  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.905  -1.212   1.546  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.914  -1.359   0.079  1.00  0.00           H  
HETATM   15  H4  UNL     1      -0.594  -2.131  -0.335  1.00  0.00           H  
HETATM   16  H5  UNL     1      -1.104  -0.794  -1.386  1.00  0.00           H  
HETATM   17  H6  UNL     1       1.894  -1.490  -0.608  1.00  0.00           H  
HETATM   18  H7  UNL     1       1.446  -0.162  -1.742  1.00  0.00           H  
HETATM   19  H8  UNL     1       3.956   1.944  -0.611  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   12
CONECT    4    5   13   14
CONECT    5    6   15   16
CONECT    6    7    7    8
CONECT    8    9   17   18
CONECT    9   10   10   11
CONECT   11   19
END
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SMILES for NP0001317 (3-Oxoadipic acid)

OC(=O)CCC(=O)CC(O)=O
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INCHI for NP0001317 (3-Oxoadipic acid)

InChI=1S/C6H8O5/c7-4(3-6(10)11)1-2-5(8)9/h1-3H2,(H,8,9)(H,10,11)
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View in JSmol
Synonyms
ValueSource
3-Keto-adipateChEBI
beta-Ketoadipic acidChEBI
beta-Oxoadipic acidChEBI
3-Keto-adipic acidGenerator
b-KetoadipateGenerator
b-Ketoadipic acidGenerator
beta-KetoadipateGenerator
Β-ketoadipateGenerator
Β-ketoadipic acidGenerator
b-OxoadipateGenerator
b-Oxoadipic acidGenerator
beta-OxoadipateGenerator
Β-oxoadipateGenerator
Β-oxoadipic acidGenerator
3-OxoadipateGenerator
3-KetoadipicHMDB
3-Oxoadipic acid, disodium saltHMDB
3-KetoadipateHMDB
3-Ketoadipic acidHMDB
3-OxohexanedioateHMDB
3-Oxohexanedioic acidHMDB
3-oxo-AdipateHMDB
3-Oxoadipic acidKEGG
Chemical FormulaC6H8O5
Average Mass160.1247 Da
Monoisotopic Mass160.03717 Da
IUPAC Name3-oxohexanedioic acid
Traditional Name3-oxoadipic acid
CAS Registry Number689-31-6
SMILES
OC(=O)CCC(=O)CC(O)=O
InChI Identifier
InChI=1S/C6H8O5/c7-4(3-6(10)11)1-2-5(8)9/h1-3H2,(H,8,9)(H,10,11)
InChI KeyRTGHRDFWYQHVFW-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)varshavi.d26@gmail.comNot AvailableNot Available2021-08-11View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Plakortis simplexLOTUS Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
  • Beta-keto acid
  • 1,3-dicarbonyl compound
  • Dicarboxylic acid or derivatives
  • Beta-hydroxy ketone
  • 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 Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point124 - 126 °CNot Available
Boiling Point412.25 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-0.688 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility37.1 g/LALOGPS
logP-0.64ALOGPS
logP-0.18ChemAxon
logS-0.64ALOGPS
pKa (Strongest Acidic)3.47ChemAxon
pKa (Strongest Basic)-7.5ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area91.67 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity33.43 m³·mol⁻¹ChemAxon
Polarizability13.91 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000398
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022015
KNApSAcK IDNot Available
Chemspider ID91
KEGG Compound IDC00846
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5387
PubChem Compound93
PDB IDNot Available
ChEBI ID37440
Good Scents IDrw1192791
References
General References
  1. Svendsen JS, Sydnes LK, Whist JE: Identification of 3-oxodicarboxylic acids in human urine. J Chromatogr. 1988 Nov 18;432:13-9. [PubMed:3220884 ]
  2. SISTROM WR, STANIER RY: The mechanism of formation of beta-ketoadipic acid by bacteria. J Biol Chem. 1954 Oct;210(2):821-36. [PubMed:13211620 ]
  3. STANIER RY, SLEEPER BP, TSUCHIDA M, MACDONALD DL: The bacterial oxidation of aromatic compounds; III. The enzymatic oxidation of catechol and protocatechuic acid to beta-ketoadipic acid. J Bacteriol. 1950 Feb;59(2):137-51. doi: 10.1128/jb.59.2.137-151.1950. [PubMed:15421941 ]
  4. KILBY BA: The bacterial oxidation of phenol to beta-ketoadipic acid. Biochem J. 1948;43(1):v. [PubMed:18933507 ]
  5. Shin JH, Andersen AJC, Achterberg P, Olsson L: Exploring functionality of the reverse beta-oxidation pathway in Corynebacterium glutamicum for production of adipic acid. Microb Cell Fact. 2021 Aug 4;20(1):155. doi: 10.1186/s12934-021-01647-7. [PubMed:34348702 ]
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