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Showing metabocard for Tetranor-PGJM (HMDB0341399)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:56:08 UTC
Update Date2022-09-22 18:34:53 UTC
HMDB IDHMDB0341399
Secondary Accession NumbersNone
Metabolite Identification
Common NameTetranor-PGJM
DescriptionTetranor-PGJM 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-PGJM.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341399 (Tetranor-PGJM)


  Mrv1652309092223342D          

 24 24  0  0  1  0            999 V2000
    2.1325    0.5288    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9877    1.3410    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3297    0.8432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5697    1.1642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0882    0.6665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8482    0.9874    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0138   -0.1522    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9718    2.1658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7513    2.4359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2490    1.7779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0739    1.7938    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7771    1.1012    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5943    0.9879    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0471    0.3217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5070   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7771   -1.0815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2370   -1.7052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5872   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1273   -0.6138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9374   -0.7697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4775   -0.1461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2877   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8278    0.3217    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5577   -1.0815    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
M  END
Download

3D MOL for HMDB0341399 (Tetranor-PGJM)

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3D SDF for HMDB0341399 (Tetranor-PGJM)

  Mrv1652309092223342D          

 24 24  0  0  1  0            999 V2000
    2.1325    0.5288    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9877    1.3410    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3297    0.8432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5697    1.1642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0882    0.6665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8482    0.9874    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0138   -0.1522    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9718    2.1658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7513    2.4359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2490    1.7779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0739    1.7938    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7771    1.1012    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5943    0.9879    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0471    0.3217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5070   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7771   -1.0815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2370   -1.7052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5872   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1273   -0.6138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9374   -0.7697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4775   -0.1461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2877   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8278    0.3217    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5577   -1.0815    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341399

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C16H22O6/c17-12(3-1-2-4-15(19)20)7-8-13-11(5-9-14(13)18)6-10-16(21)22/h5,9,11,13H,1-4,6-8,10H2,(H,19,20)(H,21,22)/t11-,13-/m1/s1

> <INCHI_KEY>
KPFBKANRLYZJQP-DGCLKSJQSA-N

> <FORMULA>
C16H22O6

> <MOLECULAR_WEIGHT>
310.346

> <EXACT_MASS>
310.141638428

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
32.78545604058658

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8-[(1R,2S)-2-(2-carboxyethyl)-5-oxocyclopent-3-en-1-yl]-6-oxooctanoic acid

> <JCHEM_LOGP>
2.0528711936666673

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.659720206056777

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.044844261876155

> <JCHEM_PKA_STRONGEST_BASIC>
-4.927870306895457

> <JCHEM_POLAR_SURFACE_AREA>
108.74000000000001

> <JCHEM_REFRACTIVITY>
79.24399999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
8-[(1R,2S)-2-(2-carboxyethyl)-5-oxocyclopent-3-en-1-yl]-6-oxooctanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341399 (Tetranor-PGJM)
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PDB for HMDB0341399 (Tetranor-PGJM)
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  H   UNK     0       3.981   0.987   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       3.710   2.503   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.482   1.574   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.063   2.173   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.165   1.244   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.583   1.843   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.026  -0.284   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       3.681   4.043   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.136   4.547   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.065   3.319   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       7.605   3.348   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.184   2.056   0.000  0.00  0.00           C+0
HETATM   13  H   UNK     0       6.709   1.844   0.000  0.00  0.00           H+0
HETATM   14  C   UNK     0       5.688   0.600   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.680  -0.564   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.184  -2.019   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.176  -3.183   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.696  -2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.704  -1.146   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.217  -1.437   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.225  -0.273   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.737  -0.564   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      12.745   0.600   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      12.241  -2.019   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8   12                                             
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    2    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    2   13   14                                             
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END

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3D PDB for HMDB0341399 (Tetranor-PGJM)
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SMILES for HMDB0341399 (Tetranor-PGJM)
[H][C@]1(CCC(O)=O)C=CC(=O)[C@]1([H])CCC(=O)CCCCC(O)=O
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INCHI for HMDB0341399 (Tetranor-PGJM)
InChI=1S/C16H22O6/c17-12(3-1-2-4-15(19)20)7-8-13-11(5-9-14(13)18)6-10-16(21)22/h5,9,11,13H,1-4,6-8,10H2,(H,19,20)(H,21,22)/t11-,13-/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-[(1R,2S)-2-(2-carboxyethyl)-5-oxocyclopent-3-en-1-yl]-6-oxooctanoic acid
Traditional Name8-[(1R,2S)-2-(2-carboxyethyl)-5-oxocyclopent-3-en-1-yl]-6-oxooctanoic acid
CAS Registry NumberNot Available
SMILES
[H][C@]1(CCC(O)=O)C=CC(=O)[C@]1([H])CCC(=O)CCCCC(O)=O
InChI Identifier
InChI=1S/C16H22O6/c17-12(3-1-2-4-15(19)20)7-8-13-11(5-9-14(13)18)6-10-16(21)22/h5,9,11,13H,1-4,6-8,10H2,(H,19,20)(H,21,22)/t11-,13-/m1/s1
InChI KeyKPFBKANRLYZJQP-DGCLKSJQSA-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
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Cyclic ketone
    • 

  • Ketone
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic 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
logP2.05ChemAxon
pKa (Strongest Acidic)4.04ChemAxon
pKa (Strongest Basic)-4.9ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area108.74 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity79.24 m³·mol⁻¹ChemAxon
Polarizability32.79 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
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 ID29341942  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound58060656  
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  ]