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Showing metabocard for (2Z)-5-hydroxydec-2-enoic acid (HMDB0340532)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2022-07-09 00:03:23 UTC
Update Date2022-07-09 00:03:23 UTC
HMDB IDHMDB0340532
Secondary Accession NumbersNone
Metabolite Identification
Common Name(2Z)-5-hydroxydec-2-enoic acid
Description(Z)-5-hydroxydec-2-enoic Acid 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 (Z)-5-hydroxydec-2-enoic Acid is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for HMDB0340532 ((2Z)-5-hydroxydec-2-enoic acid)


  Mrv1652304102100172D          

 13 12  0  0  0  0            999 V2000
    1.0461   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618   -0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763   -0.1914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -0.1914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  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
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
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3D MOL for HMDB0340532 ((2Z)-5-hydroxydec-2-enoic acid)

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3D SDF for HMDB0340532 ((2Z)-5-hydroxydec-2-enoic acid)

  Mrv1652304102100172D          

 13 12  0  0  0  0            999 V2000
    1.0461   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618   -0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763   -0.1914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -0.1914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  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
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0340532

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCC(O)C\C=C/C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H18O3/c1-2-3-4-6-9(11)7-5-8-10(12)13/h5,8-9,11H,2-4,6-7H2,1H3,(H,12,13)/b8-5-

> <INCHI_KEY>
PZLPREJERJHZHZ-YVMONPNESA-N

> <FORMULA>
C10H18O3

> <MOLECULAR_WEIGHT>
186.251

> <EXACT_MASS>
186.12559444

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
20.92498339213286

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2Z)-5-hydroxydec-2-enoic acid

> <ALOGPS_LOGP>
2.62

> <JCHEM_LOGP>
2.2002757503333332

> <ALOGPS_LOGS>
-2.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.47008273450714

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.784872469534039

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2809862435484067

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
52.24040000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.55e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2Z)-5-hydroxydec-2-enoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0340532 ((2Z)-5-hydroxydec-2-enoic acid)
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PDB for HMDB0340532 ((2Z)-5-hydroxydec-2-enoic acid)
HEADER    PROTEIN                                 10-APR-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-APR-21         0                                  
HETATM    1  C   UNK     0       1.953  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.286  -3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954  -3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.287  -2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.621  -3.437   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.621  -4.977   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.955  -2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.288  -3.437   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.622  -2.667   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.622  -1.127   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      13.956  -0.357   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      11.288  -0.357   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

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3D PDB for HMDB0340532 ((2Z)-5-hydroxydec-2-enoic acid)
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SMILES for HMDB0340532 ((2Z)-5-hydroxydec-2-enoic acid)
CCCCCC(O)C\C=C/C(O)=O
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INCHI for HMDB0340532 ((2Z)-5-hydroxydec-2-enoic acid)
InChI=1S/C10H18O3/c1-2-3-4-6-9(11)7-5-8-10(12)13/h5,8-9,11H,2-4,6-7H2,1H3,(H,12,13)/b8-5-
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(Z)-5-Hydroxydec-2-enoateGenerator
Chemical FormulaC10H18O3
Average Molecular Weight186.251
Monoisotopic Molecular Weight186.12559444
IUPAC Name(2Z)-5-hydroxydec-2-enoic acid
Traditional Name(2Z)-5-hydroxydec-2-enoic acid
CAS Registry NumberNot Available
SMILES
CCCCCC(O)C\C=C/C(O)=O
InChI Identifier
InChI=1S/C10H18O3/c1-2-3-4-6-9(11)7-5-8-10(12)13/h5,8-9,11H,2-4,6-7H2,1H3,(H,12,13)/b8-5-
InChI KeyPZLPREJERJHZHZ-YVMONPNESA-N
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
    • 

  • Hydroxy fatty acid
    • 

  • Unsaturated fatty acid
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot 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
PropertyValueSource
logP2.62ALOGPS
logP2.2ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)4.78ChemAxon
pKa (Strongest Basic)-1.3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity52.24 m³·mol⁻¹ChemAxon
Polarizability20.92 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Kovats Retention Indices
Not Available
Spectra
GC-MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - (2Z)-5-hydroxydec-2-enoic acid GC-MS (TMS_2_1) - 70eV, PositiveNot Available2022-08-08Wishart LabView Spectrum
MS/MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (2Z)-5-hydroxydec-2-enoic acid  10V, Positive-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (2Z)-5-hydroxydec-2-enoic acid  20V, Positive-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (2Z)-5-hydroxydec-2-enoic acid  40V, Positive-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (2Z)-5-hydroxydec-2-enoic acid  10V, Negative-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (2Z)-5-hydroxydec-2-enoic acid  20V, Negative-QTOFNot Available2022-08-10Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (2Z)-5-hydroxydec-2-enoic acid  40V, Negative-QTOFNot Available2022-08-10Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID9943926  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11769243  
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 ReferencesNot Available