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Showing metabocard for 3-hydroxystachydrine (HMDB0341257)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:00:36 UTC
Update Date2022-09-22 18:34:43 UTC
HMDB IDHMDB0341257
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-hydroxystachydrine
Description3-hydroxystachydrine belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Based on a literature review very few articles have been published on 3-hydroxystachydrine.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341257 (3-hydroxystachydrine)


  Mrv1652309151715582D          

 11 11  0  0  1  0            999 V2000
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 C   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
  2  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  5 10  1  0  0  0  0
  2 11  1  0  0  0  0
M  CHG  2   2   1   9  -1
M  END
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3D MOL for HMDB0341257 (3-hydroxystachydrine)

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3D SDF for HMDB0341257 (3-hydroxystachydrine)

  Mrv1652309151715582D          

 11 11  0  0  1  0            999 V2000
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 C   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
  2  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  5 10  1  0  0  0  0
  2 11  1  0  0  0  0
M  CHG  2   2   1   9  -1
M  END
> <DATABASE_ID>
HMDB0341257

> <DATABASE_NAME>
hmdb

> <SMILES>
C[N+]1(C)CCC(O)[C@H]1C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H13NO3/c1-8(2)4-3-5(9)6(8)7(10)11/h5-6,9H,3-4H2,1-2H3/t5?,6-/m0/s1

> <INCHI_KEY>
DJMIFDZBCUUQJN-GDVGLLTNSA-N

> <FORMULA>
C7H13NO3

> <MOLECULAR_WEIGHT>
159.185

> <EXACT_MASS>
159.089543283

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
15.85363633755981

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-3-hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate

> <ALOGPS_LOGP>
-1.43

> <JCHEM_LOGP>
-5.024127701138411

> <ALOGPS_LOGS>
-1.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.130689957672523

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.021729377611736

> <JCHEM_PKA_STRONGEST_BASIC>
-3.744738202784414

> <JCHEM_POLAR_SURFACE_AREA>
60.36

> <JCHEM_REFRACTIVITY>
61.4276

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.20e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341257 (3-hydroxystachydrine)
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PDB for HMDB0341257 (3-hydroxystachydrine)
HEADER    PROTEIN                                 15-SEP-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-SEP-17         0                                  
HETATM    1  C   UNK     0       0.029   3.224   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.060   2.080   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.795   0.620   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.971   3.157   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.090   3.224   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6   11                                             
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    2    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    5                                                            
CONECT   11    2                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for HMDB0341257 (3-hydroxystachydrine)
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SMILES for HMDB0341257 (3-hydroxystachydrine)
C[N+]1(C)CCC(O)[C@H]1C([O-])=O
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INCHI for HMDB0341257 (3-hydroxystachydrine)
InChI=1S/C7H13NO3/c1-8(2)4-3-5(9)6(8)7(10)11/h5-6,9H,3-4H2,1-2H3/t5?,6-/m0/s1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC7H13NO3
Average Molecular Weight159.185
Monoisotopic Molecular Weight159.089543283
IUPAC Name(2S)-3-hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate
Traditional Name(2S)-3-hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate
CAS Registry NumberNot Available
SMILES
C[N+]1(C)CCC(O)[C@H]1C([O-])=O
InChI Identifier
InChI=1S/C7H13NO3/c1-8(2)4-3-5(9)6(8)7(10)11/h5-6,9H,3-4H2,1-2H3/t5?,6-/m0/s1
InChI KeyDJMIFDZBCUUQJN-GDVGLLTNSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentProline and derivatives  
Alternative Parents
Substituents
  • Proline or derivatives
    • 

  • Alpha-amino acid
    • 

  • L-alpha-amino acid
    • 

  • Pyrrolidine carboxylic acid
    • 

  • Pyrrolidine carboxylic acid or derivatives
    • 

  • Beta-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • N-alkylpyrrolidine
    • 

  • Tetraalkylammonium salt
    • 

  • Pyrrolidine
    • 

  • Quaternary ammonium salt
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid salt
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Organic salt
    • 

  • Organic nitrogen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP-1.4ALOGPS
logP-5ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)2.02ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area60.36 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity61.43 m³·mol⁻¹ChemAxon
Polarizability15.85 ųChemAxon
Number of Rings1ChemAxon
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
MS/MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxystachydrine  10V, Positive-QTOFsplash10-03di-0900000000-7ec8e1f91e85b23192272019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxystachydrine  20V, Positive-QTOFsplash10-03di-1900000000-de45789137c89433ccbc2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxystachydrine  40V, Positive-QTOFsplash10-0avi-9000000000-5f6235a88bd8ea1fa1cd2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxystachydrine  10V, Negative-QTOFsplash10-0a4i-0900000000-5bb052a4ef0ce8b634192019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxystachydrine  20V, Negative-QTOFsplash10-0a4i-1900000000-cfad1b055fe2aadfbeac2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxystachydrine  40V, Negative-QTOFsplash10-0a4i-9000000000-8f7f0bff3719480fc0e82019-02-23Wishart LabView Spectrum
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 IDC00002045  
Chemspider ID30791164  
KEGG Compound IDC10151  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound46173781  
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  ]