Hmdb loader

Showing metabocard for Marrubiin (HMDB0341338)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:31:36 UTC
Update Date2022-09-22 18:34:49 UTC
HMDB IDHMDB0341338
Secondary Accession NumbersNone
Metabolite Identification
Common NameMarrubiin
DescriptionMarrubiin belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. Based on a literature review a significant number of articles have been published on Marrubiin.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for HMDB0341338 (Marrubiin)


  Mrv1652309092223092D          

 27 30  0  0  1  0            999 V2000
    1.6051   -0.3412    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6913    0.4793    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9377    0.1437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8514   -0.6767    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7652   -1.4972    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0978   -1.0123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5189   -1.1617    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9802   -1.8456    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9254   -1.7347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1250   -2.5352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9180   -2.7626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5681   -2.2547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2521   -2.7161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0247   -3.5091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2002   -3.5379    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2725   -0.8261    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3019   -1.6506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1987   -1.1617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8661   -0.6767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7799    0.1437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0262    0.4793    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6393    1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7713    1.2639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2562    1.9314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9463    1.2639    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3588   -0.0056    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0732   -0.4181    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  6  0  0  0
  4  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 11 15  1  0  0  0  0
  7 16  1  0  0  0  0
 16 17  1  1  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  6  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
  2 25  1  0  0  0  0
 21 26  1  0  0  0  0
  2 26  1  0  0  0  0
 16 26  1  0  0  0  0
 26 27  1  6  0  0  0
M  END
Download

3D MOL for HMDB0341338 (Marrubiin)

Download
3D SDF for HMDB0341338 (Marrubiin)

  Mrv1652309092223092D          

 27 30  0  0  1  0            999 V2000
    1.6051   -0.3412    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6913    0.4793    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9377    0.1437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8514   -0.6767    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7652   -1.4972    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0978   -1.0123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5189   -1.1617    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9802   -1.8456    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9254   -1.7347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1250   -2.5352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9180   -2.7626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5681   -2.2547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2521   -2.7161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0247   -3.5091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2002   -3.5379    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2725   -0.8261    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3019   -1.6506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1987   -1.1617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8661   -0.6767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7799    0.1437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0262    0.4793    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6393    1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7713    1.2639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2562    1.9314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9463    1.2639    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3588   -0.0056    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0732   -0.4181    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  6  0  0  0
  4  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 11 15  1  0  0  0  0
  7 16  1  0  0  0  0
 16 17  1  1  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  6  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
  2 25  1  0  0  0  0
 21 26  1  0  0  0  0
  2 26  1  0  0  0  0
 16 26  1  0  0  0  0
 26 27  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0341338

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@]12C[C@@]([H])(C)[C@](O)(CCC3=COC=C3)[C@@]3(C)CCC[C@](C)(C(=O)O1)[C@]23[H]

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O4/c1-13-11-15-16-18(2,17(21)24-15)7-4-8-19(16,3)20(13,22)9-5-14-6-10-23-12-14/h6,10,12-13,15-16,22H,4-5,7-9,11H2,1-3H3/t13-,15-,16+,18+,19+,20-/m1/s1

> <INCHI_KEY>
HQLLRHCTVDVUJB-OBHOOXMTSA-N

> <FORMULA>
C20H28O4

> <MOLECULAR_WEIGHT>
332.44

> <EXACT_MASS>
332.198759382

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
36.07430960744018

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,4S,8S,9R,10R,12R)-9-[2-(furan-3-yl)ethyl]-9-hydroxy-4,8,10-trimethyl-2-oxatricyclo[6.3.1.0^{4,12}]dodecan-3-one

> <JCHEM_LOGP>
3.757252853666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.171482542909505

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7860097992315023

> <JCHEM_POLAR_SURFACE_AREA>
59.67

> <JCHEM_REFRACTIVITY>
89.77799999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,4S,8S,9R,10R,12R)-9-[2-(furan-3-yl)ethyl]-9-hydroxy-4,8,10-trimethyl-2-oxatricyclo[6.3.1.0^{4,12}]dodecan-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for HMDB0341338 (Marrubiin)
Download
PDB for HMDB0341338 (Marrubiin)
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       2.996  -0.637   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       3.157   0.895   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.750   0.268   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.589  -1.263   0.000  0.00  0.00           C+0
HETATM    5  H   UNK     0       1.428  -2.795   0.000  0.00  0.00           H+0
HETATM    6  C   UNK     0       0.182  -1.890   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.835  -2.168   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.696  -3.445   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.727  -3.238   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.100  -4.732   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.580  -5.157   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.794  -4.209   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       6.071  -5.070   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       5.646  -6.550   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.107  -6.604   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.242  -1.542   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.297  -3.081   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.971  -2.168   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.217  -1.263   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.056   0.268   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.649   0.895   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.793   1.925   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.173   2.359   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       6.078   3.605   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       3.633   2.359   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       4.403  -0.010   0.000  0.00  0.00           C+0
HETATM   27  H   UNK     0       5.737  -0.780   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3   25   26                                             
CONECT    3    2    4                                                       
CONECT    4    3    5    6    7                                             
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    4    8    9   16                                             
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   15                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   11                                                       
CONECT   16    7   17   18   26                                             
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23   26                                             
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23    2                                                       
CONECT   26   21    2   16   27                                             
CONECT   27   26                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   60    0
END

Download
3D PDB for HMDB0341338 (Marrubiin)
Download
SMILES for HMDB0341338 (Marrubiin)
[H][C@]12C[C@@]([H])(C)[C@](O)(CCC3=COC=C3)[C@@]3(C)CCC[C@](C)(C(=O)O1)[C@]23[H]
Download
INCHI for HMDB0341338 (Marrubiin)
InChI=1S/C20H28O4/c1-13-11-15-16-18(2,17(21)24-15)7-4-8-19(16,3)20(13,22)9-5-14-6-10-23-12-14/h6,10,12-13,15-16,22H,4-5,7-9,11H2,1-3H3/t13-,15-,16+,18+,19+,20-/m1/s1
Download
View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC20H28O4
Average Molecular Weight332.44
Monoisotopic Molecular Weight332.198759382
IUPAC Name(1R,4S,8S,9R,10R,12R)-9-[2-(furan-3-yl)ethyl]-9-hydroxy-4,8,10-trimethyl-2-oxatricyclo[6.3.1.0^{4,12}]dodecan-3-one
Traditional Name(1R,4S,8S,9R,10R,12R)-9-[2-(furan-3-yl)ethyl]-9-hydroxy-4,8,10-trimethyl-2-oxatricyclo[6.3.1.0^{4,12}]dodecan-3-one
CAS Registry NumberNot Available
SMILES
[H][C@]12C[C@@]([H])(C)[C@](O)(CCC3=COC=C3)[C@@]3(C)CCC[C@](C)(C(=O)O1)[C@]23[H]
InChI Identifier
InChI=1S/C20H28O4/c1-13-11-15-16-18(2,17(21)24-15)7-4-8-19(16,3)20(13,22)9-5-14-6-10-23-12-14/h6,10,12-13,15-16,22H,4-5,7-9,11H2,1-3H3/t13-,15-,16+,18+,19+,20-/m1/s1
InChI KeyHQLLRHCTVDVUJB-OBHOOXMTSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassLactones  
Sub ClassGamma butyrolactones  
Direct ParentGamma butyrolactones  
Alternative Parents
Substituents
  • Gamma butyrolactone
    • 

  • Cyclic alcohol
    • 

  • Furan
    • 

  • Heteroaromatic compound
    • 

  • Tetrahydrofuran
    • 

  • Tertiary alcohol
    • 

  • Carboxylic acid ester
    • 

  • Carboxylic acid derivative
    • 

  • Oxacycle
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Organooxygen compound
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
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
logP3.76ChemAxon
pKa (Strongest Acidic)14.17ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area59.67 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity89.78 m³·mol⁻¹ChemAxon
Polarizability36.07 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 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 IDC00003452  
Chemspider ID66118  
KEGG Compound IDC09128  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound73401  
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1699721  
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  ]