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Showing metabocard for 3-hydroxy-C12 homoserine lactone (HMDB0341118)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 19:10:06 UTC
Update Date2022-09-22 18:35:00 UTC
HMDB IDHMDB0341118
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-hydroxy-C12 homoserine lactone
Description3-hydroxy-C12 homoserine lactone belongs to the class of organic compounds known as n-acyl-alpha amino acids and derivatives. N-acyl-alpha amino acids and derivatives are compounds containing an alpha amino acid (or a derivative thereof) which bears an acyl group at its terminal nitrogen atom. Based on a literature review a significant number of articles have been published on 3-hydroxy-C12 homoserine lactone.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341118 (3-hydroxy-C12 homoserine lactone)


  Mrv1652309092221482D          

 21 21  0  0  0  0            999 V2000
    4.9202   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6346   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3491   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0636   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7781   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4925   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2070   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9215   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6359   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3504   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3504   -7.0578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0649   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7794   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7794   -7.0578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4938   -5.8203    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.2083   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9620   -5.8972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5140   -6.5103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1015   -7.2248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2945   -7.0533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6814   -7.6053    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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  4  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 16 20  1  0  0  0  0
 20 21  2  0  0  0  0
M  END
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3D MOL for HMDB0341118 (3-hydroxy-C12 homoserine lactone)

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3D SDF for HMDB0341118 (3-hydroxy-C12 homoserine lactone)

  Mrv1652309092221482D          

 21 21  0  0  0  0            999 V2000
    4.9202   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6346   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3491   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0636   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7781   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4925   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2070   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9215   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6359   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3504   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3504   -7.0578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0649   -5.8203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7794   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7794   -7.0578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4938   -5.8203    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.2083   -6.2328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9620   -5.8972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5140   -6.5103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1015   -7.2248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2945   -7.0533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6814   -7.6053    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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  4  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 16 20  1  0  0  0  0
 20 21  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341118

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCCC(O)CC(O)=NC1CCOC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H29NO4/c1-2-3-4-5-6-7-8-9-13(18)12-15(19)17-14-10-11-21-16(14)20/h13-14,18H,2-12H2,1H3,(H,17,19)

> <INCHI_KEY>
RGTXFFYJJNWEPV-UHFFFAOYSA-N

> <FORMULA>
C16H29NO4

> <MOLECULAR_WEIGHT>
299.411

> <EXACT_MASS>
299.209658418

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
34.6436038167469

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-hydroxy-N-(2-oxooxolan-3-yl)dodecanimidic acid

> <JCHEM_LOGP>
3.2081030773333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.28642477671709

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.398211962406924

> <JCHEM_PKA_STRONGEST_BASIC>
1.3450385926890593

> <JCHEM_POLAR_SURFACE_AREA>
79.12

> <JCHEM_REFRACTIVITY>
80.93109999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-N-(2-oxooxolan-3-yl)dodecanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341118 (3-hydroxy-C12 homoserine lactone)
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PDB for HMDB0341118 (3-hydroxy-C12 homoserine lactone)
HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       9.184 -10.865   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.518 -11.635   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.852 -10.865   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.185 -11.635   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.519 -10.865   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      15.853 -11.635   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      17.186 -10.865   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.520 -11.635   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      19.854 -10.865   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      21.187 -11.635   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      21.187 -13.175   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      22.521 -10.865   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      23.855 -11.635   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      23.855 -13.175   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0      25.188 -10.865   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      26.522 -11.635   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      27.929 -11.008   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      28.959 -12.153   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      28.189 -13.486   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      26.683 -13.166   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      25.539 -14.197   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                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   20                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   16   21                                                  
CONECT   21   20                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

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3D PDB for HMDB0341118 (3-hydroxy-C12 homoserine lactone)
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SMILES for HMDB0341118 (3-hydroxy-C12 homoserine lactone)
CCCCCCCCCC(O)CC(O)=NC1CCOC1=O
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INCHI for HMDB0341118 (3-hydroxy-C12 homoserine lactone)
InChI=1S/C16H29NO4/c1-2-3-4-5-6-7-8-9-13(18)12-15(19)17-14-10-11-21-16(14)20/h13-14,18H,2-12H2,1H3,(H,17,19)
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC16H29NO4
Average Molecular Weight299.411
Monoisotopic Molecular Weight299.209658418
IUPAC Name3-hydroxy-N-(2-oxooxolan-3-yl)dodecanimidic acid
Traditional Name3-hydroxy-N-(2-oxooxolan-3-yl)dodecanimidic acid
CAS Registry NumberNot Available
SMILES
CCCCCCCCCC(O)CC(O)=NC1CCOC1=O
InChI Identifier
InChI=1S/C16H29NO4/c1-2-3-4-5-6-7-8-9-13(18)12-15(19)17-14-10-11-21-16(14)20/h13-14,18H,2-12H2,1H3,(H,17,19)
InChI KeyRGTXFFYJJNWEPV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as n-acyl-alpha amino acids and derivatives. N-acyl-alpha amino acids and derivatives are compounds containing an alpha amino acid (or a derivative thereof) which bears an acyl group at its terminal nitrogen atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentN-acyl-alpha amino acids and derivatives  
Alternative Parents
Substituents
  • Alpha-amino acid ester
    • 

  • N-acyl-alpha amino acid or derivatives
    • 

  • Acyl-homoserine lactone
    • 

  • Fatty amide
    • 

  • Gamma butyrolactone
    • 

  • N-acyl-amine
    • 

  • Fatty acyl
    • 

  • Oxolane
    • 

  • Carboxamide group
    • 

  • Carboxylic acid ester
    • 

  • Lactone
    • 

  • Secondary alcohol
    • 

  • Secondary carboxylic acid amide
    • 

  • Oxacycle
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organoheterocyclic compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Alcohol
    • 

  • Organic nitrogen compound
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP3.21ChemAxon
pKa (Strongest Acidic)5.4ChemAxon
pKa (Strongest Basic)1.35ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area79.12 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity80.93 m³·mol⁻¹ChemAxon
Polarizability34.64 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
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
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal  details
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 ID9682474  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11507677  
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. Neto FC, Raftery D: Expanding Urinary Metabolite Annotation through Integrated Mass Spectral Similarity Networking. Anal Chem. 2021 Sep 7;93(35):12001-12010. doi: 10.1021/acs.analchem.1c02041. Epub 2021 Aug 26. [PubMed:34436864  ]