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Showing metabocard for 2,2-Bis(hydroxymethyl)-3-quinuclidinone (HMDB0341243)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 19:55:42 UTC
Update Date2022-09-22 18:34:42 UTC
HMDB IDHMDB0341243
Secondary Accession NumbersNone
Metabolite Identification
Common Name2,2-Bis(hydroxymethyl)-3-quinuclidinone
Description2,2-Bis(hydroxymethyl)-3-quinuclidinone belongs to the class of organic compounds known as quinuclidones. Quinuclidones are compounds containing a quinuclidine moiety which bears a ketone group. Based on a literature review very few articles have been published on 2,2-Bis(hydroxymethyl)-3-quinuclidinone.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341243 (2,2-Bis(hydroxymethyl)-3-quinuclidinone)


  Mrv1652309092222332D          

 13 14  0  0  0  0            999 V2000
    1.0030    0.3834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0030    0.9334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1405    1.4834    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4260    1.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4260    0.2459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1405   -0.1666    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8549    0.2459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5694   -0.1666    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8549    1.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6794    1.0997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667    1.8282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2921    1.7706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9048    2.4990    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
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
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3D MOL for HMDB0341243 (2,2-Bis(hydroxymethyl)-3-quinuclidinone)

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3D SDF for HMDB0341243 (2,2-Bis(hydroxymethyl)-3-quinuclidinone)

  Mrv1652309092222332D          

 13 14  0  0  0  0            999 V2000
    1.0030    0.3834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0030    0.9334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1405    1.4834    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4260    1.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4260    0.2459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1405   -0.1666    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8549    0.2459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5694   -0.1666    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8549    1.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6794    1.0997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667    1.8282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2921    1.7706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9048    2.4990    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
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341243

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1(CO)N2CCC(CC2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H15NO3/c11-5-9(6-12)8(13)7-1-3-10(9)4-2-7/h7,11-12H,1-6H2

> <INCHI_KEY>
RFBVBRVVOPAAFS-UHFFFAOYSA-N

> <FORMULA>
C9H15NO3

> <MOLECULAR_WEIGHT>
185.223

> <EXACT_MASS>
185.105193347

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
18.90978600111226

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,2-bis(hydroxymethyl)-1-azabicyclo[2.2.2]octan-3-one

> <JCHEM_LOGP>
-0.7980551490000001

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.931979527096463

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.233834440261045

> <JCHEM_PKA_STRONGEST_BASIC>
5.692132944297815

> <JCHEM_POLAR_SURFACE_AREA>
60.77000000000001

> <JCHEM_REFRACTIVITY>
47.656600000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
2,2-bis(hydroxymethyl)-1-azabicyclo[2.2.2]octan-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341243 (2,2-Bis(hydroxymethyl)-3-quinuclidinone)
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PDB for HMDB0341243 (2,2-Bis(hydroxymethyl)-3-quinuclidinone)
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       1.872   0.716   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.872   1.742   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.129   2.769   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.795   1.999   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.795   0.459   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.129  -0.311   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.463   0.459   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.796  -0.311   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       3.463   1.999   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.002   2.053   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       5.725   3.413   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.279   3.305   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.556   4.665   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    3   10   12                                             
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13                                                       
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END

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3D PDB for HMDB0341243 (2,2-Bis(hydroxymethyl)-3-quinuclidinone)
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SMILES for HMDB0341243 (2,2-Bis(hydroxymethyl)-3-quinuclidinone)
OCC1(CO)N2CCC(CC2)C1=O
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INCHI for HMDB0341243 (2,2-Bis(hydroxymethyl)-3-quinuclidinone)
InChI=1S/C9H15NO3/c11-5-9(6-12)8(13)7-1-3-10(9)4-2-7/h7,11-12H,1-6H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2,2-Bis(hydroxymethyl)-1-azabicyclo(2,2,2,)octan-3-oneMeSH
Chemical FormulaC9H15NO3
Average Molecular Weight185.223
Monoisotopic Molecular Weight185.105193347
IUPAC Name2,2-bis(hydroxymethyl)-1-azabicyclo[2.2.2]octan-3-one
Traditional Name2,2-bis(hydroxymethyl)-1-azabicyclo[2.2.2]octan-3-one
CAS Registry NumberNot Available
SMILES
OCC1(CO)N2CCC(CC2)C1=O
InChI Identifier
InChI=1S/C9H15NO3/c11-5-9(6-12)8(13)7-1-3-10(9)4-2-7/h7,11-12H,1-6H2
InChI KeyRFBVBRVVOPAAFS-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as quinuclidones. Quinuclidones are compounds containing a quinuclidine moiety which bears a ketone group.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassQuinuclidines  
Sub ClassQuinuclidones  
Direct ParentQuinuclidones  
Alternative Parents
Substituents
  • Quinuclidone
    • 

  • Piperidinone
    • 

  • Piperidine
    • 

  • Ketone
    • 

  • Tertiary amine
    • 

  • Tertiary aliphatic amine
    • 

  • Azacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Primary alcohol
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • Alcohol
    • 

  • 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
logP-0.8ChemAxon
pKa (Strongest Acidic)14.23ChemAxon
pKa (Strongest Basic)5.69ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area60.77 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity47.66 m³·mol⁻¹ChemAxon
Polarizability18.91 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Retention Times 
Not Available
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 ID285992  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound322968  
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  ]