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Showing metabocard for Bicyclo[2.1.0]pentane (HMDB0249189)

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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
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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
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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
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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

$$$$
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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
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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
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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
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SMILES for HMDB0249189 (Bicyclo[2.1.0]pentane)

C1C2CCC12
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INCHI for HMDB0249189 (Bicyclo[2.1.0]pentane)

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