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Showing metabocard for 3-Hydroxyadipic acid (HMDB0000345)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:44 UTC
HMDB IDHMDB0000345
Secondary Accession Numbers
  • HMDB00345
Metabolite Identification
Common Name3-Hydroxyadipic acid
Description3-Hydroxyadipic acid, also known as 3-hydroxyadipate, belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain. 3-Hydroxyadipic acid has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 3-hydroxyadipic acid a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 3-Hydroxyadipic acid.
Structure
Data?1676999684
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000345 (3-Hydroxyadipic acid)

  Mrv0541 02231218282D          

 11 10  0  0  0  0            999 V2000
   12.8187  -15.7898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.9622  -14.5523    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9608  -14.9648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2477  -15.7898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6753  -13.7272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8187  -14.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1043  -14.5523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5333  -14.5523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3898  -14.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2477  -14.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6753  -14.5523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2 10  1  0  0  0  0
  3 11  1  0  0  0  0
  4 10  2  0  0  0  0
  5 11  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
M  END
Download

3D MOL for HMDB0000345 (3-Hydroxyadipic acid)

HMDB0000345
     RDKit          3D
3-Hydroxyadipic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -1.8097    1.1147   -1.6325 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4593    0.2536   -1.0083 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6837   -0.1427   -1.5005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9274   -0.3312    0.2345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5889    0.2001    0.6183 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5100   -0.0116   -0.3595 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6864   -1.3674   -0.5675 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7779    0.5857    0.2626 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9138    0.4020   -0.6720 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0592    1.2055   -1.6243 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7779   -0.6628   -0.4511 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5405    0.2444   -1.1082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9453   -1.4514    0.1863 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6017   -0.1046    1.1150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2889   -0.3328    1.5683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6750    1.2632    0.9057 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4056    0.4550   -1.3355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0002   -1.9405   -0.1796 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0027    0.1389    1.2478 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6342    1.6799    0.4042 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7529   -1.1979    0.3876 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  1  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
  6 17  1  0
  7 18  1  0
  8 19  1  0
  8 20  1  0
 11 21  1  0
M  END
Download

3D SDF for HMDB0000345 (3-Hydroxyadipic acid)

  Mrv0541 02231218282D          

 11 10  0  0  0  0            999 V2000
   12.8187  -15.7898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.9622  -14.5523    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9608  -14.9648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2477  -15.7898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6753  -13.7272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8187  -14.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1043  -14.5523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5333  -14.5523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3898  -14.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2477  -14.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6753  -14.5523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2 10  1  0  0  0  0
  3 11  1  0  0  0  0
  4 10  2  0  0  0  0
  5 11  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000345

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O5/c7-4(3-6(10)11)1-2-5(8)9/h4,7H,1-3H2,(H,8,9)(H,10,11)

> <INCHI_KEY>
YVOMYDHIQVMMTA-UHFFFAOYSA-N

> <FORMULA>
C6H10O5

> <MOLECULAR_WEIGHT>
162.1406

> <EXACT_MASS>
162.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
14.77758062589532

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxyhexanedioic acid

> <ALOGPS_LOGP>
-0.89

> <JCHEM_LOGP>
-0.7401567043333332

> <ALOGPS_LOGS>
-0.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.456438347376524

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6988469573165053

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8079016560382133

> <JCHEM_POLAR_SURFACE_AREA>
94.82999999999998

> <JCHEM_REFRACTIVITY>
34.2545

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.82e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxyadipic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000345 (3-Hydroxyadipic acid)

HMDB0000345
     RDKit          3D
3-Hydroxyadipic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -1.8097    1.1147   -1.6325 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4593    0.2536   -1.0083 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6837   -0.1427   -1.5005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9274   -0.3312    0.2345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5889    0.2001    0.6183 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5100   -0.0116   -0.3595 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6864   -1.3674   -0.5675 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7779    0.5857    0.2626 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9138    0.4020   -0.6720 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0592    1.2055   -1.6243 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7779   -0.6628   -0.4511 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5405    0.2444   -1.1082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9453   -1.4514    0.1863 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6017   -0.1046    1.1150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2889   -0.3328    1.5683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6750    1.2632    0.9057 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4056    0.4550   -1.3355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0002   -1.9405   -0.1796 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0027    0.1389    1.2478 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6342    1.6799    0.4042 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7529   -1.1979    0.3876 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  1  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
  6 17  1  0
  7 18  1  0
  8 19  1  0
  8 20  1  0
 11 21  1  0
M  END
Download

PDB for HMDB0000345 (3-Hydroxyadipic acid)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      23.928 -29.474   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      27.929 -27.164   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      18.593 -27.934   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      26.596 -29.474   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      19.927 -25.624   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      23.928 -27.934   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.595 -27.164   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      25.262 -27.164   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.261 -27.934   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      26.596 -27.934   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      19.927 -27.164   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4   10                                                            
CONECT    5   11                                                            
CONECT    6    1    7    8                                                  
CONECT    7    6    9                                                       
CONECT    8    6   10                                                       
CONECT    9    7   11                                                       
CONECT   10    2    4    8                                                  
CONECT   11    3    5    9                                                  
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0000345 (3-Hydroxyadipic acid)

COMPND    HMDB0000345
HETATM    1  O1  UNL     1      -1.810   1.115  -1.633  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.459   0.254  -1.008  1.00  0.00           C  
HETATM    3  O2  UNL     1      -3.684  -0.143  -1.500  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.927  -0.331   0.234  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.589   0.200   0.618  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.510  -0.012  -0.359  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.686  -1.367  -0.567  1.00  0.00           O  
HETATM    8  C5  UNL     1       1.778   0.586   0.263  1.00  0.00           C  
HETATM    9  C6  UNL     1       2.914   0.402  -0.672  1.00  0.00           C  
HETATM   10  O4  UNL     1       3.059   1.206  -1.624  1.00  0.00           O  
HETATM   11  O5  UNL     1       3.778  -0.663  -0.451  1.00  0.00           O  
HETATM   12  H1  UNL     1      -4.541   0.244  -1.108  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.945  -1.451   0.186  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.602  -0.105   1.115  1.00  0.00           H  
HETATM   15  H4  UNL     1      -0.289  -0.333   1.568  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.675   1.263   0.906  1.00  0.00           H  
HETATM   17  H6  UNL     1       0.406   0.455  -1.336  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.000  -1.940  -0.180  1.00  0.00           H  
HETATM   19  H8  UNL     1       2.003   0.139   1.248  1.00  0.00           H  
HETATM   20  H9  UNL     1       1.634   1.680   0.404  1.00  0.00           H  
HETATM   21  H10 UNL     1       3.753  -1.198   0.388  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    8   17
CONECT    7   18
CONECT    8    9   19   20
CONECT    9   10   10   11
CONECT   11   21
END
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SMILES for HMDB0000345 (3-Hydroxyadipic acid)

OC(CCC(O)=O)CC(O)=O
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INCHI for HMDB0000345 (3-Hydroxyadipic acid)

InChI=1S/C6H10O5/c7-4(3-6(10)11)1-2-5(8)9/h4,7H,1-3H2,(H,8,9)(H,10,11)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-HydroxyadipateGenerator
(3S)-3-HydroxyadipateHMDB
(3S)-3-Hydroxyadipic acidHMDB
3-HydroxyhexanedioateHMDB
3-Hydroxyhexanedioic acidHMDB
3-Hydroxy-adipateHMDB
3-Hydroxyadipic acidMeSH
Chemical FormulaC6H10O5
Average Molecular Weight162.1406
Monoisotopic Molecular Weight162.05282343
IUPAC Name3-hydroxyhexanedioic acid
Traditional Name3-hydroxyadipic acid
CAS Registry Number14292-29-6
SMILES
OC(CCC(O)=O)CC(O)=O
InChI Identifier
InChI=1S/C6H10O5/c7-4(3-6(10)11)1-2-5(8)9/h4,7H,1-3H2,(H,8,9)(H,10,11)
InChI KeyYVOMYDHIQVMMTA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassMedium-chain hydroxy acids and derivatives
Direct ParentMedium-chain hydroxy acids and derivatives
Alternative Parents
Substituents
  • Medium-chain hydroxy acid
  • Medium-chain fatty acid
  • Beta-hydroxy acid
  • Hydroxy fatty acid
  • Dicarboxylic acid or derivatives
  • Fatty acyl
  • Fatty acid
  • Secondary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Carbonyl group
  • Organic oxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
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
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified47.416-340.978 umol/mmol creatinineInfant (0-1 year old)Not Specified3-Hydroxydicarboxylic aciduria details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease References
3-Hydroxydicarboxylic aciduria
  1. Tserng KY, Jin SJ, Kerr DS, Hoppel CL: Urinary 3-hydroxydicarboxylic acids in pathophysiology of metabolic disorders with dicarboxylic aciduria. Metabolism. 1991 Jul;40(7):676-82. [PubMed:1870421 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021968
KNApSAcK IDNot Available
Chemspider ID133894
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5334
PubChem Compound151913
PDB IDNot Available
ChEBI ID89205
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceChiruta, Chandramouli; Jachak, Santosh; Clive, Derrick L. J. A convenient general method for the synthesis of hydroxy diacids. Tetrahedron Letters (2007), 48(18), 3141-3143.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. [PubMed:8087979 ]
  2. Bennett MJ, Ragni MC, Hood I, Hale DE: Comparison of post-mortem urinary and vitreous humour organic acids. Ann Clin Biochem. 1992 Sep;29 ( Pt 5):541-5. [PubMed:1444166 ]
  3. Svendsen JS, Whist JE, Sydnes LK: Absolute configuration of 3-hydroxyadipic acid in human urine. J Chromatogr. 1985 Jan 11;337(1):9-19. [PubMed:3980660 ]
  4. Tserng KY, Jin SJ: Metabolic origin of urinary 3-hydroxy dicarboxylic acids. Biochemistry. 1991 Mar 5;30(9):2508-14. [PubMed:2001377 ]
  5. Grupe A, Spiteller G: New polar acid metabolites in human urine. J Chromatogr. 1981 Dec 11;226(2):301-14. [PubMed:7320161 ]
  6. Tserng KY, Jin SJ, Hoppel CL, Kerr DS, Genuth SM: Urinary 3-hydroxyadipic acid 3,6-lactone: structural identification and effect of fasting in adults and children. Metabolism. 1989 Jul;38(7):655-61. [PubMed:2739576 ]
  7. Kelley RI, Morton DH: 3-Hydroxyoctanoic aciduria: identification of a new organic acid in the urine of a patient with non-ketotic hypoglycemia. Clin Chim Acta. 1988 Jun 30;175(1):19-26. [PubMed:3168281 ]