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Showing metabocard for Tetranor-PGDM lactone (HMDB0341398)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:55:40 UTC
Update Date2022-09-22 18:34:53 UTC
HMDB IDHMDB0341398
Secondary Accession NumbersNone
Metabolite Identification
Common NameTetranor-PGDM lactone
DescriptionTetranor-PGDM lactone 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. Based on a literature review very few articles have been published on Tetranor-PGDM lactone.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341398 (Tetranor-PGDM lactone)


  Mrv1652309092223332D          

 22 23  0  0  1  0            999 V2000
   -2.6392   -0.8802    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6392   -1.7052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3537   -2.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0681   -1.7052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7826   -2.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4971   -1.7052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2116   -2.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9260   -1.7052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2116   -2.9427    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9247   -2.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2103   -1.7052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4958   -2.1177    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4095   -2.9382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3974   -3.1097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8099   -2.3952    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2579   -1.7821    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5128   -0.9975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3198   -0.8260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8718   -1.4391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6169   -2.2237    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6788   -1.2676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0226   -3.4902    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  7  9  2  0  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  1  0  0  0
 15 16  1  0  0  0  0
 12 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
 19 21  2  0  0  0  0
 13 22  2  0  0  0  0
M  END
Download

3D MOL for HMDB0341398 (Tetranor-PGDM lactone)

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3D SDF for HMDB0341398 (Tetranor-PGDM lactone)

  Mrv1652309092223332D          

 22 23  0  0  1  0            999 V2000
   -2.6392   -0.8802    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6392   -1.7052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3537   -2.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0681   -1.7052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7826   -2.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4971   -1.7052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2116   -2.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9260   -1.7052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2116   -2.9427    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9247   -2.1177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2103   -1.7052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4958   -2.1177    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4095   -2.9382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3974   -3.1097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8099   -2.3952    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2579   -1.7821    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5128   -0.9975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3198   -0.8260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8718   -1.4391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6169   -2.2237    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6788   -1.2676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0226   -3.4902    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  7  9  2  0  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  1  0  0  0
 15 16  1  0  0  0  0
 12 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
 19 21  2  0  0  0  0
 13 22  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341398

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CCCCC(=O)CC[C@@H]1[C@H]2CCC(=O)O[C@H]2CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H22O6/c17-10(3-1-2-4-15(19)20)5-6-11-12-7-8-16(21)22-14(12)9-13(11)18/h11-12,14H,1-9H2,(H,19,20)/t11-,12-,14+/m1/s1

> <INCHI_KEY>
KRZCZJUXOKTLEH-BZPMIXESSA-N

> <FORMULA>
C16H22O6

> <MOLECULAR_WEIGHT>
310.346

> <EXACT_MASS>
310.141638428

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
32.30988080699356

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8-[(4aR,5R,7aS)-2,6-dioxo-octahydrocyclopenta[b]pyran-5-yl]-6-oxooctanoic acid

> <JCHEM_LOGP>
1.5666614916666668

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.09126756018632

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.427070777520253

> <JCHEM_PKA_STRONGEST_BASIC>
-6.770519047242816

> <JCHEM_POLAR_SURFACE_AREA>
97.73999999999998

> <JCHEM_REFRACTIVITY>
76.09699999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
8-[(4aR,5R,7aS)-2,6-dioxo-hexahydrocyclopenta[b]pyran-5-yl]-6-oxooctanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341398 (Tetranor-PGDM lactone)
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PDB for HMDB0341398 (Tetranor-PGDM 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  O   UNK     0      -4.926  -1.643   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -4.926  -3.183   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -6.260  -3.953   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -7.594  -3.183   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -8.928  -3.953   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -10.261  -3.183   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -11.595  -3.953   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0     -12.929  -3.183   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0     -11.595  -5.493   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -3.593  -3.953   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.259  -3.183   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.925  -3.953   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.764  -5.485   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.742  -5.805   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.512  -4.471   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.481  -3.327   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.957  -1.862   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.464  -1.542   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.494  -2.686   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       3.018  -4.151   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       5.000  -2.366   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -1.909  -6.515   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    2   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   16                                                  
CONECT   13   12   14   22                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   12   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19   15                                                       
CONECT   21   19                                                            
CONECT   22   13                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

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3D PDB for HMDB0341398 (Tetranor-PGDM lactone)
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SMILES for HMDB0341398 (Tetranor-PGDM lactone)
OC(=O)CCCCC(=O)CC[C@@H]1[C@H]2CCC(=O)O[C@H]2CC1=O
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INCHI for HMDB0341398 (Tetranor-PGDM lactone)
InChI=1S/C16H22O6/c17-10(3-1-2-4-15(19)20)5-6-11-12-7-8-16(21)22-14(12)9-13(11)18/h11-12,14H,1-9H2,(H,19,20)/t11-,12-,14+/m1/s1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC16H22O6
Average Molecular Weight310.346
Monoisotopic Molecular Weight310.141638428
IUPAC Name8-[(4aR,5R,7aS)-2,6-dioxo-octahydrocyclopenta[b]pyran-5-yl]-6-oxooctanoic acid
Traditional Name8-[(4aR,5R,7aS)-2,6-dioxo-hexahydrocyclopenta[b]pyran-5-yl]-6-oxooctanoic acid
CAS Registry NumberNot Available
SMILES
OC(=O)CCCCC(=O)CC[C@@H]1[C@H]2CCC(=O)O[C@H]2CC1=O
InChI Identifier
InChI=1S/C16H22O6/c17-10(3-1-2-4-15(19)20)5-6-11-12-7-8-16(21)22-14(12)9-13(11)18/h11-12,14H,1-9H2,(H,19,20)/t11-,12-,14+/m1/s1
InChI KeyKRZCZJUXOKTLEH-BZPMIXESSA-N
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
    • 

  • Delta valerolactone
    • 

  • Heterocyclic fatty acid
    • 

  • Delta_valerolactone
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Fatty acyl
    • 

  • Oxane
    • 

  • Carboxylic acid ester
    • 

  • Ketone
    • 

  • Lactone
    • 

  • Cyclic ketone
    • 

  • Oxacycle
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organoheterocyclic compound
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic 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
logP1.57ChemAxon
pKa (Strongest Acidic)4.43ChemAxon
pKa (Strongest Basic)-6.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area97.74 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity76.1 m³·mol⁻¹ChemAxon
Polarizability32.31 ųChemAxon
Number of Rings2ChemAxon
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
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID29341943  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound68011454  
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. Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920  ]