Hmdb loader

Showing metabocard for Bicyclo[2.1.0]pentane (HMDB0249189)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 03:40:57 UTC
Update Date2021-09-26 22:59:54 UTC
HMDB IDHMDB0249189
Secondary Accession NumbersNone
Metabolite Identification
Common NameBicyclo[2.1.0]pentane
DescriptionBicyclo[2.1.0]pentane belongs to the class of organic compounds known as polycyclic hydrocarbons. These are polycyclic organic compounds made up only of carbon and hydrogen atoms. Based on a literature review a significant number of articles have been published on Bicyclo[2.1.0]pentane. This compound has been identified in human blood as reported by (PMID: 31557052 ). Bicyclo[2.1.0]pentane is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Bicyclo[2.1.0]pentane 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0249189 (Bicyclo[2.1.0]pentane)


  Mrv1652309112105412D          

  5  6  0  0  0  0            999 V2000
    1.4757    1.4757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4757    0.6507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6507    0.6507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6507    1.4757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0638    1.0632    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
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0249189 (Bicyclo[2.1.0]pentane)

HMDB0249189
     RDKit          3D
Bicyclo[2.1.0]pentane
 13 14  0  0  0  0  0  0  0  0999 V2000
   -0.8989    0.7656    0.4211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0002   -0.7151    0.2125 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3101   -0.7133   -0.5160 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5216   -0.0590    0.1241 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3951    0.7435   -0.3381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8453    1.0536    1.4839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6716    1.3877   -0.0794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8314   -0.9720   -0.4704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9392   -1.3500    1.1092 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -1.2278   -1.4746 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6362   -0.2731    1.2061 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4188   -0.1037   -0.5259 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4921    1.4635   -1.1525 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
  5  3  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
  4 12  1  0
  5 13  1  0
M  END
Download

3D SDF for HMDB0249189 (Bicyclo[2.1.0]pentane)


  Mrv1652309112105412D          

  5  6  0  0  0  0            999 V2000
    1.4757    1.4757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4757    0.6507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6507    0.6507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6507    1.4757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0638    1.0632    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
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0249189

> <DATABASE_NAME>
hmdb

> <SMILES>
C1C2CCC12

> <INCHI_IDENTIFIER>
InChI=1S/C5H8/c1-2-5-3-4(1)5/h4-5H,1-3H2

> <INCHI_KEY>
MHLPKAGDPWUOOT-UHFFFAOYSA-N

> <FORMULA>
C5H8

> <MOLECULAR_WEIGHT>
68.119

> <EXACT_MASS>
68.062600258

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
8.50360648297502

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
bicyclo[2.1.0]pentane

> <ALOGPS_LOGP>
2.06

> <JCHEM_LOGP>
1.444018285

> <ALOGPS_LOGS>
-1.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
21.098

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.78e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
bicyclo[2.1.0]pentane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0249189 (Bicyclo[2.1.0]pentane)

HMDB0249189
     RDKit          3D
Bicyclo[2.1.0]pentane
 13 14  0  0  0  0  0  0  0  0999 V2000
   -0.8989    0.7656    0.4211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0002   -0.7151    0.2125 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3101   -0.7133   -0.5160 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5216   -0.0590    0.1241 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3951    0.7435   -0.3381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8453    1.0536    1.4839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6716    1.3877   -0.0794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8314   -0.9720   -0.4704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9392   -1.3500    1.1092 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -1.2278   -1.4746 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6362   -0.2731    1.2061 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4188   -0.1037   -0.5259 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4921    1.4635   -1.1525 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
  5  3  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
  4 12  1  0
  5 13  1  0
M  END
Download

PDB for HMDB0249189 (Bicyclo[2.1.0]pentane)

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       2.755   2.755   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.755   1.215   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.215   1.215   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.215   2.755   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.119   1.985   0.000  0.00  0.00           C+0
CONECT    1    2    4                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3    1    5                                                  
CONECT    5    4    3                                                       
MASTER        0    0    0    0    0    0    0    0    5    0   12    0
END
Download

3D PDB for HMDB0249189 (Bicyclo[2.1.0]pentane)

COMPND    HMDB0249189
HETATM    1  C1  UNL     1      -0.899   0.766   0.421  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.000  -0.715   0.213  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.310  -0.713  -0.516  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.522  -0.059   0.124  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.395   0.743  -0.338  1.00  0.00           C  
HETATM    6  H1  UNL     1      -0.845   1.054   1.484  1.00  0.00           H  
HETATM    7  H2  UNL     1      -1.672   1.388  -0.079  1.00  0.00           H  
HETATM    8  H3  UNL     1      -1.831  -0.972  -0.470  1.00  0.00           H  
HETATM    9  H4  UNL     1      -0.939  -1.350   1.109  1.00  0.00           H  
HETATM   10  H5  UNL     1       0.413  -1.228  -1.475  1.00  0.00           H  
HETATM   11  H6  UNL     1       1.636  -0.273   1.206  1.00  0.00           H  
HETATM   12  H7  UNL     1       2.419  -0.104  -0.526  1.00  0.00           H  
HETATM   13  H8  UNL     1       0.492   1.464  -1.152  1.00  0.00           H  
CONECT    1    2    5    6    7
CONECT    2    3    8    9
CONECT    3    4    5   10
CONECT    4    5   11   12
CONECT    5   13
END
Download

SMILES for HMDB0249189 (Bicyclo[2.1.0]pentane)

C1C2CCC12
Download

INCHI for HMDB0249189 (Bicyclo[2.1.0]pentane)

InChI=1S/C5H8/c1-2-5-3-4(1)5/h4-5H,1-3H2
Download
View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC5H8
Average Molecular Weight68.119
Monoisotopic Molecular Weight68.062600258
IUPAC Namebicyclo[2.1.0]pentane
Traditional Namebicyclo[2.1.0]pentane
CAS Registry NumberNot Available
SMILES
C1C2CCC12
InChI Identifier
InChI=1S/C5H8/c1-2-5-3-4(1)5/h4-5H,1-3H2
InChI KeyMHLPKAGDPWUOOT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as polycyclic hydrocarbons. These are polycyclic organic compounds made up only of carbon and hydrogen atoms.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassPolycyclic hydrocarbons
Sub ClassNot Available
Direct ParentPolycyclic hydrocarbons
Alternative Parents
Substituents
  • Polycyclic hydrocarbon
  • Saturated hydrocarbon
  • Aliphatic homopolycyclic compound
Molecular FrameworkAliphatic homopolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
logP2.06ALOGPS
logP1.44ChemAxon
logS-1.9ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity21.1 m³·mol⁻¹ChemAxon
Polarizability8.5 ųChemAxon
Number of Rings2ChemAxon
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-2H]-155.3930932474
DeepCCS[M+Na]+129.79730932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202213.938 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.37 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1591.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid565.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid220.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid386.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid323.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid478.8 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid588.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)469.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1049.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid346.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1085.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid373.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid392.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate649.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA473.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water143.3 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Bicyclo[2.1.0]pentaneC1C2CCC12618.5Standard polar33892256
Bicyclo[2.1.0]pentaneC1C2CCC12608.0Standard non polar33892256
Bicyclo[2.1.0]pentaneC1C2CCC12538.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Bicyclo[2.1.0]pentane GC-MS (Non-derivatized) - 70eV, Positivesplash10-002f-9000000000-0d4c8385653db2e6651a2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Bicyclo[2.1.0]pentane GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclo[2.1.0]pentane 10V, Positive-QTOFsplash10-014i-9000000000-974cc4f003ec9d1686532021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclo[2.1.0]pentane 20V, Positive-QTOFsplash10-014i-9000000000-9ac974c89b315cc8bb542021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclo[2.1.0]pentane 40V, Positive-QTOFsplash10-0fr6-9000000000-490196f7dde32f4dfdf12021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclo[2.1.0]pentane 10V, Negative-QTOFsplash10-014i-9000000000-cd562456e37b5675ece72021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclo[2.1.0]pentane 20V, Negative-QTOFsplash10-014i-9000000000-1f51f38f38eefa83c9ee2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclo[2.1.0]pentane 40V, Negative-QTOFsplash10-014i-9000000000-889e8b95182dda1225712021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart 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 ID8747
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9101
PDB IDNot Available
ChEBI ID49287
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 ]