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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2022-07-09 00:18:34 UTC

Update Date

2022-07-09 00:18:34 UTC

HMDB ID

HMDB0340579

Secondary Accession Numbers

None

Metabolite Identification

Common Name

3-hydroxydecanedioic acid

Description

3-Hydroxysebacic acid, also known as 3-hydroxy-sebacate or 3-hydroxydecanedioic acid, 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-Hydroxysebacic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 3-Hydroxysebacic acid, with regard to humans, has been linked to the inborn metabolic disorder medium chain acyl-coa dehydrogenase deficiency.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305261923572D          

 15 14  0  0  0  0            999 V2000
   20.2436  -16.1263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.3871  -14.8888    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5277  -15.3013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.6726  -16.1263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2422  -14.0637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.8146  -15.3013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1002  -14.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.5291  -14.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.3856  -15.3013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.2436  -15.3013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6712  -14.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.9581  -14.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9567  -15.3013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.6726  -15.3013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2422  -14.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2 14  1  0  0  0  0
  3 15  1  0  0  0  0
  4 14  2  0  0  0  0
  5 15  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
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0340579

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H18O5/c11-8(7-10(14)15)5-3-1-2-4-6-9(12)13/h8,11H,1-7H2,(H,12,13)(H,14,15)

> <INCHI_KEY>
OQYZCCKCJQWHIE-UHFFFAOYSA-N

> <FORMULA>
C10H18O5

> <MOLECULAR_WEIGHT>
218.2469

> <EXACT_MASS>
218.115423686

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
23.362731405302434

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-hydroxydecanedioic acid

> <ALOGPS_LOGP>
0.63

> <JCHEM_LOGP>
1.0381179556666666

> <ALOGPS_LOGS>
-1.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.052863606302775

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.450063494495128

> <JCHEM_PKA_STRONGEST_BASIC>
-2.798587427000225

> <JCHEM_POLAR_SURFACE_AREA>
94.82999999999998

> <JCHEM_REFRACTIVITY>
52.658500000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.38e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxysebacic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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  O   UNK     0      37.788 -30.102   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      41.789 -27.792   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      27.118 -28.562   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      40.456 -30.102   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      28.452 -26.252   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      35.121 -28.562   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      33.787 -27.792   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      36.454 -27.792   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      32.453 -28.562   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      37.788 -28.562   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      31.120 -27.792   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      39.122 -27.792   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      29.786 -28.562   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      40.456 -28.562   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      28.452 -27.792   0.000  0.00  0.00           C+0
CONECT    1   10                                                            
CONECT    2   14                                                            
CONECT    3   15                                                            
CONECT    4   14                                                            
CONECT    5   15                                                            
CONECT    6    7    8                                                       
CONECT    7    6    9                                                       
CONECT    8    6   10                                                       
CONECT    9    7   11                                                       
CONECT   10    1    8   12                                                  
CONECT   11    9   13                                                       
CONECT   12   10   14                                                       
CONECT   13   11   15                                                       
CONECT   14    2    4   12                                                  
CONECT   15    3    5   13                                                  
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3-Hydroxy-decanedioic acid	ChEBI
3-Hydroxy-sebacic acid	ChEBI
3-Hydroxy-decanedioate	Generator
3-Hydroxy-sebacate	Generator
3-Hydroxysebacate	Generator
3-Hydroxydecanedioate	HMDB
3-Hydroxydecanedioic acid	HMDB

Chemical Formula

C₁₀H₁₈O₅

Average Molecular Weight

218.2469

Monoisotopic Molecular Weight

218.115423686

IUPAC Name

3-hydroxydecanedioic acid

Traditional Name

3-hydroxysebacic acid

CAS Registry Number

Not Available

SMILES

OC(CCCCCCC(O)=O)CC(O)=O

InChI Identifier

InChI=1S/C10H18O5/c11-8(7-10(14)15)5-3-1-2-4-6-9(12)13/h8,11H,1-7H2,(H,12,13)(H,14,15)

InChI Key

OQYZCCKCJQWHIE-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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Medium-chain hydroxy acids and derivatives

Direct Parent

Medium-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 Framework

Aliphatic acyclic compounds

External Descriptors

Dicarboxylic acids (LMFA01170092 )

Ontology

Not Available

Not Available

Not Available

Not Available

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	0.63	ALOGPS
logP	1.04	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	4.45	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	52.66 m³·mol⁻¹	ChemAxon
Polarizability	23.36 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

Predicted Chromatographic Properties

Predicted Kovats Retention Indices

Not Available

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3-hydroxydecanedioic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-052f-9710000000-84f7737e071eed92f742	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-hydroxydecanedioic acid GC-MS (3 TMS) - 70eV, Positive	splash10-01e9-7459200000-a1f5613b57112c5d2584	2017-10-06	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3-hydroxydecanedioic acid Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-0159-0940000000-f4f483b1636137e43945	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3-hydroxydecanedioic acid Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-014m-9400000000-d0cc01c70aafa53f34ab	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3-hydroxydecanedioic acid Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-00mo-9000000000-316ddd132092b08d73b4	2012-07-24	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxydecanedioic acid 10V, Positive-QTOF	splash10-0ue9-0690000000-adfdd11672c699fbe0b3	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxydecanedioic acid 20V, Positive-QTOF	splash10-0pc0-1920000000-04e756075b530fdc1c35	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxydecanedioic acid 40V, Positive-QTOF	splash10-0a4l-9500000000-28ce1a7d162f222ab3da	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxydecanedioic acid 10V, Negative-QTOF	splash10-014j-0960000000-dc3ec12cde243eb68c4a	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxydecanedioic acid 20V, Negative-QTOF	splash10-0aba-0910000000-50719a409f05424fe56d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-hydroxydecanedioic acid 40V, Negative-QTOF	splash10-0a4i-9800000000-8f1d999d507005531c7d	2017-09-01	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CD₃OD, experimental)	2012-12-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB021973

KNApSAcK ID

Not Available

Chemspider ID

2285525

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5339

PubChem Compound

3017884

PDB ID

Not Available

ChEBI ID

89182

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for 3-hydroxydecanedioic acid (HMDB0340579)

MOL for HMDB0340579 (3-hydroxydecanedioic acid)

3D MOL for HMDB0340579 (3-hydroxydecanedioic acid)

3D SDF for HMDB0340579 (3-hydroxydecanedioic acid)

3D-SDF for HMDB0340579 (3-hydroxydecanedioic acid)

PDB for HMDB0340579 (3-hydroxydecanedioic acid)

3D PDB for HMDB0340579 (3-hydroxydecanedioic acid)

SMILES for HMDB0340579 (3-hydroxydecanedioic acid)

INCHI for HMDB0340579 (3-hydroxydecanedioic acid)

Structure for HMDB0340579 (3-hydroxydecanedioic acid)

3D Structure for HMDB0340579 (3-hydroxydecanedioic acid)

Predicted Kovats Retention Indices

GC-MS Spectra

MS/MS Spectra

NMR Spectra