Hmdb loader

Showing metabocard for Cyclopropane (HMDB0250673)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 07:46:08 UTC
Update Date2021-10-01 19:59:27 UTC
HMDB IDHMDB0250673
Secondary Accession NumbersNone
Metabolite Identification
Common NameCyclopropane
Descriptioncyclopropane, also known as trimethylene, belongs to the class of organic compounds known as cycloalkanes. These are saturated monocyclic hydrocarbons (with or without side chains). Based on a literature review very few articles have been published on cyclopropane. This compound has been identified in human blood as reported by (PMID: 31557052 ). Cyclopropane is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Cyclopropane 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 HMDB0250673 (Cyclopropane)


  Mrv1572004191601082D          

  3  3  0  0  0  0            999 V2000
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
M  END
Download

3D MOL for HMDB0250673 (Cyclopropane)

HMDB0250673
     RDKit          3D
Cyclopropane
  9  9  0  0  0  0  0  0  0  0999 V2000
    0.7678   -0.3851   -0.0963 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0383    0.8634    0.0917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7089   -0.4906   -0.0296 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3287   -0.4938   -1.0407 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3101   -0.7956    0.7773 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2441    1.5291   -0.7510 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0560    1.3291    1.0935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1802   -0.8349    0.8952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2911   -0.7216   -0.9401 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  1  1  0
  1  4  1  0
  1  5  1  0
  2  6  1  0
  2  7  1  0
  3  8  1  0
  3  9  1  0
M  END
Download

3D SDF for HMDB0250673 (Cyclopropane)


  Mrv1572004191601082D          

  3  3  0  0  0  0            999 V2000
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250673

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CC1

> <INCHI_IDENTIFIER>
InChI=1S/C3H6/c1-2-3-1/h1-3H2

> <INCHI_KEY>
LVZWSLJZHVFIQJ-UHFFFAOYSA-N

> <FORMULA>
C3H6

> <MOLECULAR_WEIGHT>
42.081

> <EXACT_MASS>
42.046950193

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
5.512278077382804

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cyclopropane

> <ALOGPS_LOGP>
1.56

> <JCHEM_LOGP>
1.333705995

> <ALOGPS_LOGS>
-0.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
13.803

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.01e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyclopropane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0250673 (Cyclopropane)

HMDB0250673
     RDKit          3D
Cyclopropane
  9  9  0  0  0  0  0  0  0  0999 V2000
    0.7678   -0.3851   -0.0963 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0383    0.8634    0.0917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7089   -0.4906   -0.0296 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3287   -0.4938   -1.0407 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3101   -0.7956    0.7773 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2441    1.5291   -0.7510 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0560    1.3291    1.0935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1802   -0.8349    0.8952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2911   -0.7216   -0.9401 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  1  1  0
  1  4  1  0
  1  5  1  0
  2  6  1  0
  2  7  1  0
  3  8  1  0
  3  9  1  0
M  END
Download

PDB for HMDB0250673 (Cyclopropane)

HEADER    PROTEIN                                 19-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-16         0                                  
HETATM    1  C   UNK     0       1.215   0.325   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.445   1.659   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.325   0.325   0.000  0.00  0.00           C+0
CONECT    1    2    3                                                       
CONECT    2    1    3                                                       
CONECT    3    1    2                                                       
MASTER        0    0    0    0    0    0    0    0    3    0    6    0
END
Download

3D PDB for HMDB0250673 (Cyclopropane)

COMPND    HMDB0250673
HETATM    1  C1  UNL     1       0.768  -0.385  -0.096  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.038   0.863   0.092  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.709  -0.491  -0.030  1.00  0.00           C  
HETATM    4  H1  UNL     1       1.329  -0.494  -1.041  1.00  0.00           H  
HETATM    5  H2  UNL     1       1.310  -0.796   0.777  1.00  0.00           H  
HETATM    6  H3  UNL     1      -0.244   1.529  -0.751  1.00  0.00           H  
HETATM    7  H4  UNL     1       0.056   1.329   1.094  1.00  0.00           H  
HETATM    8  H5  UNL     1      -1.180  -0.835   0.895  1.00  0.00           H  
HETATM    9  H6  UNL     1      -1.291  -0.722  -0.940  1.00  0.00           H  
CONECT    1    2    3    4    5
CONECT    2    3    6    7
CONECT    3    8    9
END
Download

SMILES for HMDB0250673 (Cyclopropane)

C1CC1
Download

INCHI for HMDB0250673 (Cyclopropane)

InChI=1S/C3H6/c1-2-3-1/h1-3H2
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
CiclopropanoChEBI
CyclopropanChEBI
CyclopropanumChEBI
TrimethyleneChEBI
ZyklopropanChEBI
Chemical FormulaC3H6
Average Molecular Weight42.081
Monoisotopic Molecular Weight42.046950193
IUPAC Namecyclopropane
Traditional Namecyclopropane
CAS Registry NumberNot Available
SMILES
C1CC1
InChI Identifier
InChI=1S/C3H6/c1-2-3-1/h1-3H2
InChI KeyLVZWSLJZHVFIQJ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cycloalkanes. These are saturated monocyclic hydrocarbons (with or without side chains).
KingdomOrganic compounds
Super ClassHydrocarbons
ClassSaturated hydrocarbons
Sub ClassCycloalkanes
Direct ParentCycloalkanes
Alternative ParentsNot Available
Substituents
  • Cycloalkane
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic 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
logP1.56ALOGPS
logP1.33ChemAxon
logS-0.62ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity13.8 m³·mol⁻¹ChemAxon
Polarizability5.51 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]+117.70830932474
DeepCCS[M-H]-115.81330932474
DeepCCS[M-2H]-151.12230932474
DeepCCS[M+Na]+125.34130932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
CyclopropaneC1CC1397.4Standard polar33892256
CyclopropaneC1CC1372.4Standard non polar33892256
CyclopropaneC1CC1344.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cyclopropane GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9000000000-ddc041b2281b0c2b3bae2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cyclopropane 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 - Cyclopropane 10V, Positive-QTOFsplash10-0006-9000000000-348a79c7d9f471575e922016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopropane 20V, Positive-QTOFsplash10-0006-9000000000-348a79c7d9f471575e922016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopropane 40V, Positive-QTOFsplash10-0006-9000000000-9b9d8c66d7f95bc11c802016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopropane 10V, Negative-QTOFsplash10-0006-9000000000-9e2a1dc0ca2b4aaa0ce92016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopropane 20V, Negative-QTOFsplash10-0006-9000000000-c1105b5989105a57f3ee2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopropane 40V, Negative-QTOFsplash10-0006-9000000000-6698c555fbb76f2b43732016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopropane 10V, Negative-QTOFsplash10-0006-9000000000-69af536d3fa1e0fd98192021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopropane 20V, Negative-QTOFsplash10-0006-9000000000-69af536d3fa1e0fd98192021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopropane 40V, Negative-QTOFsplash10-0006-9000000000-69af536d3fa1e0fd98192021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopropane 10V, Positive-QTOFsplash10-0006-9000000000-5381c9dfee7dd1735ffd2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopropane 20V, Positive-QTOFsplash10-0006-9000000000-5381c9dfee7dd1735ffd2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopropane 40V, Positive-QTOFsplash10-0006-9000000000-a720487033c471876c412021-10-12Wishart 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 IDC00000244
Chemspider ID6111
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCyclopropane
METLIN IDNot Available
PubChem Compound6351
PDB IDNot Available
ChEBI ID30365
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 ]

Enzymes

Enzyme Details
1. Probable 1-aminocyclopropane-1-carboxylate deaminase
General function:
Not Available
Specific function:
Catalyzes a cyclopropane ring-opening reaction, the irreversible conversion of 1-aminocyclopropane-1-carboxylate (ACC) to ammonia and alpha-ketobutyrate.
Gene Name:
(REFSEQ) 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE
Uniprot ID:
Q5KMX3
Molecular weight:
37049.19