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Showing metabocard for Grandisine C (HMDB0341438)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 21:11:40 UTC
Update Date2022-09-22 18:35:15 UTC
HMDB IDHMDB0341438
Secondary Accession NumbersNone
Metabolite Identification
Common NameGrandisine C
Description5-hydroxy-7-methyl-2-oxa-15-azatetracyclo[8.7.0.0³,⁸.0¹¹,¹⁵]heptadec-3(8)-en-9-one belongs to the class of organic compounds known as indolizidines. These are polycyclic compounds containing an indolizidine, which is a bicyclic heterocycle containing a saturated six-member ring fused to a saturated five-member ring, one of the bridging atoms being nitrogen. 5-hydroxy-7-methyl-2-oxa-15-azatetracyclo[8.7.0.0³,⁸.0¹¹,¹⁵]heptadec-3(8)-en-9-one is a very strong basic compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341438 (Grandisine C)


  Mrv1533004161519462D          

 20 23  0  0  0  0            999 V2000
    5.1686    1.9852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4181    1.1989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2239    1.0218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4735    0.2354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2792    0.0584    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9172   -0.3739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1115   -0.1968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8619    0.5896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0561    0.7666    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8066    1.5530    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4999    0.1573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7495   -0.6290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1932   -1.2383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3875   -1.0613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1379   -0.2749    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3865    0.0658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4784    0.8856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2865    1.0516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6941    0.3344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5552   -0.8061    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
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 11 19  1  0  0  0  0
 15 19  1  0  0  0  0
 12 20  1  0  0  0  0
  7 20  1  0  0  0  0
M  END
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3D MOL for HMDB0341438 (Grandisine C)

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3D SDF for HMDB0341438 (Grandisine C)

  Mrv1533004161519462D          

 20 23  0  0  0  0            999 V2000
    5.1686    1.9852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4181    1.1989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2239    1.0218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4735    0.2354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2792    0.0584    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9172   -0.3739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1115   -0.1968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8619    0.5896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0561    0.7666    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8066    1.5530    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4999    0.1573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7495   -0.6290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1932   -1.2383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3875   -1.0613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1379   -0.2749    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3865    0.0658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4784    0.8856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2865    1.0516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6941    0.3344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5552   -0.8061    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
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 11 19  1  0  0  0  0
 15 19  1  0  0  0  0
 12 20  1  0  0  0  0
  7 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341438

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1CC(O)CC2=C1C(=O)C1C3CCCN3CCC1O2

> <INCHI_IDENTIFIER>
InChI=1S/C16H23NO3/c1-9-7-10(18)8-13-14(9)16(19)15-11-3-2-5-17(11)6-4-12(15)20-13/h9-12,15,18H,2-8H2,1H3

> <INCHI_KEY>
WNDBXOYUMYCREE-UHFFFAOYSA-N

> <FORMULA>
C16H23NO3

> <MOLECULAR_WEIGHT>
277.364

> <EXACT_MASS>
277.167793605

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
30.68611722969073

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-hydroxy-7-methyl-2-oxa-15-azatetracyclo[8.7.0.0³,⁸.0¹¹,¹⁵]heptadec-3(8)-en-9-one

> <ALOGPS_LOGP>
0.77

> <JCHEM_LOGP>
0.5068191376666672

> <ALOGPS_LOGS>
-1.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
16.90070373044155

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.090487736831236

> <JCHEM_PKA_STRONGEST_BASIC>
9.682907716656398

> <JCHEM_POLAR_SURFACE_AREA>
49.769999999999996

> <JCHEM_REFRACTIVITY>
77.239

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.37e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxy-7-methyl-2-oxa-15-azatetracyclo[8.7.0.0³,⁸.0¹¹,¹⁵]heptadec-3(8)-en-9-one

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341438 (Grandisine C)
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PDB for HMDB0341438 (Grandisine C)
HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0       9.648   3.706   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.114   2.238   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.618   1.907   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.084   0.440   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      13.588   0.109   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      11.046  -0.698   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.541  -0.367   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.076   1.100   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.571   1.431   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       7.106   2.899   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.533   0.294   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.999  -1.174   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.961  -2.312   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.457  -1.981   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       3.991  -0.513   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       2.588   0.123   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.760   1.653   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.268   1.963   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.029   0.624   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       8.503  -1.505   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   20                                                  
CONECT    8    7    2    9                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   19                                                  
CONECT   12   11   13   20                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   19                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   11   15                                                  
CONECT   20   12    7                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   46    0
END

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3D PDB for HMDB0341438 (Grandisine C)
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SMILES for HMDB0341438 (Grandisine C)
CC1CC(O)CC2=C1C(=O)C1C3CCCN3CCC1O2
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INCHI for HMDB0341438 (Grandisine C)
InChI=1S/C16H23NO3/c1-9-7-10(18)8-13-14(9)16(19)15-11-3-2-5-17(11)6-4-12(15)20-13/h9-12,15,18H,2-8H2,1H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC16H23NO3
Average Molecular Weight277.364
Monoisotopic Molecular Weight277.167793605
IUPAC Name5-hydroxy-7-methyl-2-oxa-15-azatetracyclo[8.7.0.0³,⁸.0¹¹,¹⁵]heptadec-3(8)-en-9-one
Traditional Name5-hydroxy-7-methyl-2-oxa-15-azatetracyclo[8.7.0.0³,⁸.0¹¹,¹⁵]heptadec-3(8)-en-9-one
CAS Registry NumberNot Available
SMILES
CC1CC(O)CC2=C1C(=O)C1C3CCCN3CCC1O2
InChI Identifier
InChI=1S/C16H23NO3/c1-9-7-10(18)8-13-14(9)16(19)15-11-3-2-5-17(11)6-4-12(15)20-13/h9-12,15,18H,2-8H2,1H3
InChI KeyWNDBXOYUMYCREE-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as indolizidines. These are polycyclic compounds containing an indolizidine, which is a bicyclic heterocycle containing a saturated six-member ring fused to a saturated five-member ring, one of the bridging atoms being nitrogen.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassIndolizidines  
Sub ClassNot Available
Direct ParentIndolizidines  
Alternative Parents
Substituents
  • Indolizidine
    • 

  • Dihydropyranone
    • 

  • Piperidine
    • 

  • N-alkylpyrrolidine
    • 

  • Pyrrolidine
    • 

  • Vinylogous ester
    • 

  • Ketone
    • 

  • Secondary alcohol
    • 

  • Tertiary amine
    • 

  • Tertiary aliphatic amine
    • 

  • Oxacycle
    • 

  • Azacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Alcohol
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Amine
    • 

  • Carbonyl group
    • 

  • 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
logP0.77ALOGPS
logP0.51ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)15.09ChemAxon
pKa (Strongest Basic)9.68ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area49.77 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity77.24 m³·mol⁻¹ChemAxon
Polarizability30.69 ųChemAxon
Number of Rings4ChemAxon
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 QuantifiedAdult (>18 years old)BothAsthma  details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma  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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound73238319  
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. Meister I, Zhang P, Sinha A, Skold CM, Wheelock AM, Izumi T, Chaleckis R, Wheelock CE: High-Precision Automated Workflow for Urinary Untargeted Metabolomic Epidemiology. Anal Chem. 2021 Mar 30;93(12):5248-5258. doi: 10.1021/acs.analchem.1c00203. Epub  2021 Mar 19. [PubMed:33739820  ]