Hmdb loader

Showing metabocard for Pyrazolidine (HMDB0256949)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:35:08 UTC
Update Date2021-09-26 23:12:58 UTC
HMDB IDHMDB0256949
Secondary Accession NumbersNone
Metabolite Identification
Common NamePyrazolidine
Descriptionpyrazolidine belongs to the class of organic compounds known as pyrazolidines. Pyrazolidines are compounds containing a pyrazolidine ring, which is a five-member saturated aliphatic ring with two nitrogen atoms (at positions 1 and 2) and three carbon atoms. Based on a literature review very few articles have been published on pyrazolidine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pyrazolidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pyrazolidine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0256949 (Pyrazolidine)


  Mrv1652309112119352D          

  5  5  0  0  0  0            999 V2000
    0.5678    1.1143    0.0000 C   0  0  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 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    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
  1  5  1  0  0  0  0
M  END
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3D MOL for HMDB0256949 (Pyrazolidine)

HMDB0256949
     RDKit          3D
Pyrazolidine
 13 13  0  0  0  0  0  0  0  0999 V2000
   -0.0793   -0.8677   -0.5672 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1798   -0.1966   -0.0008 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7402    1.1908    0.0335 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5080    1.1152    0.6604 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1515   -0.0861    0.1894 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1077   -1.9395   -0.3418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1109   -0.6242   -1.6361 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0205   -0.3776   -0.6623 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3877   -0.5266    1.0214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6366    1.6027   -0.9109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4377    1.1759    1.6910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5951   -0.6910    1.0062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9747    0.2246   -0.4827 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  1  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
M  END
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3D SDF for HMDB0256949 (Pyrazolidine)


  Mrv1652309112119352D          

  5  5  0  0  0  0            999 V2000
    0.5678    1.1143    0.0000 C   0  0  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 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    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
  1  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256949

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CNNC1

> <INCHI_IDENTIFIER>
InChI=1S/C3H8N2/c1-2-4-5-3-1/h4-5H,1-3H2

> <INCHI_KEY>
USPWKWBDZOARPV-UHFFFAOYSA-N

> <FORMULA>
C3H8N2

> <MOLECULAR_WEIGHT>
72.111

> <EXACT_MASS>
72.068748266

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
7.9661710221577255

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyrazolidine

> <ALOGPS_LOGP>
-1.43

> <JCHEM_LOGP>
-0.6980034183333335

> <ALOGPS_LOGS>
0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
5.808902904839661

> <JCHEM_POLAR_SURFACE_AREA>
24.06

> <JCHEM_REFRACTIVITY>
42.119600000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.78e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrazolidine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0256949 (Pyrazolidine)

HMDB0256949
     RDKit          3D
Pyrazolidine
 13 13  0  0  0  0  0  0  0  0999 V2000
   -0.0793   -0.8677   -0.5672 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1798   -0.1966   -0.0008 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7402    1.1908    0.0335 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5080    1.1152    0.6604 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1515   -0.0861    0.1894 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1077   -1.9395   -0.3418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1109   -0.6242   -1.6361 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0205   -0.3776   -0.6623 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3877   -0.5266    1.0214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6366    1.6027   -0.9109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4377    1.1759    1.6910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5951   -0.6910    1.0062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9747    0.2246   -0.4827 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  1  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
M  END
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PDB for HMDB0256949 (Pyrazolidine)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.830  -0.290   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0       0.290  -0.290   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
MASTER        0    0    0    0    0    0    0    0    5    0   10    0
END
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3D PDB for HMDB0256949 (Pyrazolidine)

COMPND    HMDB0256949
HETATM    1  C1  UNL     1      -0.079  -0.868  -0.567  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.180  -0.197  -0.001  1.00  0.00           C  
HETATM    3  N1  UNL     1       0.740   1.191   0.033  1.00  0.00           N  
HETATM    4  N2  UNL     1      -0.508   1.115   0.660  1.00  0.00           N  
HETATM    5  C3  UNL     1      -1.152  -0.086   0.189  1.00  0.00           C  
HETATM    6  H1  UNL     1      -0.108  -1.940  -0.342  1.00  0.00           H  
HETATM    7  H2  UNL     1      -0.111  -0.624  -1.636  1.00  0.00           H  
HETATM    8  H3  UNL     1       2.021  -0.378  -0.662  1.00  0.00           H  
HETATM    9  H4  UNL     1       1.388  -0.527   1.021  1.00  0.00           H  
HETATM   10  H5  UNL     1       0.637   1.603  -0.911  1.00  0.00           H  
HETATM   11  H6  UNL     1      -0.438   1.176   1.691  1.00  0.00           H  
HETATM   12  H7  UNL     1      -1.595  -0.691   1.006  1.00  0.00           H  
HETATM   13  H8  UNL     1      -1.975   0.225  -0.483  1.00  0.00           H  
CONECT    1    2    5    6    7
CONECT    2    3    8    9
CONECT    3    4   10
CONECT    4    5   11
CONECT    5   12   13
END
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SMILES for HMDB0256949 (Pyrazolidine)

C1CNNC1
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INCHI for HMDB0256949 (Pyrazolidine)

InChI=1S/C3H8N2/c1-2-4-5-3-1/h4-5H,1-3H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,2-DiazacyclopentaneChEBI
TetrahydropyrazoleChEBI
Chemical FormulaC3H8N2
Average Molecular Weight72.111
Monoisotopic Molecular Weight72.068748266
IUPAC Namepyrazolidine
Traditional Namepyrazolidine
CAS Registry NumberNot Available
SMILES
C1CNNC1
InChI Identifier
InChI=1S/C3H8N2/c1-2-4-5-3-1/h4-5H,1-3H2
InChI KeyUSPWKWBDZOARPV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrazolidines. Pyrazolidines are compounds containing a pyrazolidine ring, which is a five-member saturated aliphatic ring with two nitrogen atoms (at positions 1 and 2) and three carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzolidines
Sub ClassPyrazolidines
Direct ParentPyrazolidines
Alternative Parents
Substituents
  • Pyrazolidine
  • Alkylhydrazine
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Hydrazine derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
RoleNot 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-0.7ChemAxon
logS0.82ALOGPS
pKa (Strongest Basic)5.81ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area24.06 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity42.12 m³·mol⁻¹ChemAxon
Polarizability7.97 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+122.14130932474
DeepCCS[M-H]-120.24630932474
DeepCCS[M-2H]-155.64730932474
DeepCCS[M+Na]+130.11230932474
AllCCS[M+H]+114.332859911
AllCCS[M+H-H2O]+109.032859911
AllCCS[M+NH4]+119.332859911
AllCCS[M+Na]+120.832859911
AllCCS[M-H]-118.832859911
AllCCS[M+Na-2H]-123.332859911
AllCCS[M+HCOO]-128.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PyrazolidineC1CNNC11326.1Standard polar33892256
PyrazolidineC1CNNC1761.7Standard non polar33892256
PyrazolidineC1CNNC1799.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Pyrazolidine,1TMS,isomer #1C[Si](C)(C)N1CCCN1974.7Semi standard non polar33892256
Pyrazolidine,1TMS,isomer #1C[Si](C)(C)N1CCCN11038.7Standard non polar33892256
Pyrazolidine,1TMS,isomer #1C[Si](C)(C)N1CCCN11570.9Standard polar33892256
Pyrazolidine,2TMS,isomer #1C[Si](C)(C)N1CCCN1[Si](C)(C)C1125.2Semi standard non polar33892256
Pyrazolidine,2TMS,isomer #1C[Si](C)(C)N1CCCN1[Si](C)(C)C1152.9Standard non polar33892256
Pyrazolidine,2TMS,isomer #1C[Si](C)(C)N1CCCN1[Si](C)(C)C1379.9Standard polar33892256
Pyrazolidine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCCN11174.1Semi standard non polar33892256
Pyrazolidine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCCN11246.5Standard non polar33892256
Pyrazolidine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCCN11743.3Standard polar33892256
Pyrazolidine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCCN1[Si](C)(C)C(C)(C)C1541.3Semi standard non polar33892256
Pyrazolidine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCCN1[Si](C)(C)C(C)(C)C1597.4Standard non polar33892256
Pyrazolidine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CCCN1[Si](C)(C)C(C)(C)C1625.4Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pyrazolidine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0096-9000000000-6fa71790140323b1c7d82021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pyrazolidine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-27Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID71365
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPyrazolidine
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID33138
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]