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Showing metabocard for Cyclooctyne (HMDB0250663)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 07:45:31 UTC
Update Date2021-09-26 23:02:16 UTC
HMDB IDHMDB0250663
Secondary Accession NumbersNone
Metabolite Identification
Common NameCyclooctyne
Descriptioncyclooctyne belongs to the class of organic compounds known as monocyclic acetylenes. These are monocyclic hydrocarbons containing one or more acetylene groups. Based on a literature review very few articles have been published on cyclooctyne. This compound has been identified in human blood as reported by (PMID: 31557052 ). Cyclooctyne is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Cyclooctyne 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 HMDB0250663 (Cyclooctyne)


  Mrv1652309112109452D          

  8  8  0  0  0  0            999 V2000
    0.9959    1.4904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7581    1.1747    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0738    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7581   -0.3497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9959   -0.6654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2337   -0.3497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0821    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2337    1.1747    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  3  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  1  8  1  0  0  0  0
M  END
Download

3D MOL for HMDB0250663 (Cyclooctyne)

HMDB0250663
     RDKit          3D
Cyclooctyne
 20 20  0  0  0  0  0  0  0  0999 V2000
    0.7019    1.2447   -0.3065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3583    1.3724   -0.3521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7803    1.2889   -0.3562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9759   -0.2776   -0.0924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6948   -0.7041    0.6220 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4658   -1.0505   -0.2249 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8154   -0.6494    0.3545 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0629    0.8380   -0.1829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1821    1.4537   -1.3559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2479    1.7911    0.4770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1440   -0.7407   -1.0470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7893   -0.3350    0.6279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4481    0.0396    1.4065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9692   -1.6537    1.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5616   -2.1806   -0.3678 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3024   -0.6828   -1.2535 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6489   -1.2601    0.0347 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8095   -0.5230    1.4419 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6551    1.3791    0.5486 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5663    0.6502   -1.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  1  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
  8 19  1  0
  8 20  1  0
M  END
Download

3D SDF for HMDB0250663 (Cyclooctyne)


  Mrv1652309112109452D          

  8  8  0  0  0  0            999 V2000
    0.9959    1.4904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7581    1.1747    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0738    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7581   -0.3497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9959   -0.6654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2337   -0.3497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0821    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2337    1.1747    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  3  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  1  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250663

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CCCC#CCC1

> <INCHI_IDENTIFIER>
InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-6H2

> <INCHI_KEY>
ZPWOOKQUDFIEIX-UHFFFAOYSA-N

> <FORMULA>
C8H12

> <MOLECULAR_WEIGHT>
108.184

> <EXACT_MASS>
108.093900386

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.501717181999329

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cyclooctyne

> <ALOGPS_LOGP>
3.91

> <JCHEM_LOGP>
3.1412559846666666

> <ALOGPS_LOGS>
-3.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
36.1694

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.42e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyclooctyne

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0250663 (Cyclooctyne)

HMDB0250663
     RDKit          3D
Cyclooctyne
 20 20  0  0  0  0  0  0  0  0999 V2000
    0.7019    1.2447   -0.3065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3583    1.3724   -0.3521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7803    1.2889   -0.3562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9759   -0.2776   -0.0924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6948   -0.7041    0.6220 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4658   -1.0505   -0.2249 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8154   -0.6494    0.3545 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0629    0.8380   -0.1829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1821    1.4537   -1.3559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2479    1.7911    0.4770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1440   -0.7407   -1.0470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7893   -0.3350    0.6279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4481    0.0396    1.4065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9692   -1.6537    1.1749 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5616   -2.1806   -0.3678 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3024   -0.6828   -1.2535 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6489   -1.2601    0.0347 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8095   -0.5230    1.4419 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6551    1.3791    0.5486 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5663    0.6502   -1.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  1  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
  8 19  1  0
  8 20  1  0
M  END
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PDB for HMDB0250663 (Cyclooctyne)

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       1.859   2.782   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.282   2.193   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.871   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.282  -0.653   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.859  -1.242   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.436  -0.653   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.153   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.436   2.193   0.000  0.00  0.00           C+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    1                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0250663 (Cyclooctyne)

COMPND    HMDB0250663
HETATM    1  C1  UNL     1       0.702   1.245  -0.306  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.358   1.372  -0.352  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.780   1.289  -0.356  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.976  -0.278  -0.092  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.695  -0.704   0.622  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.466  -1.051  -0.225  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.815  -0.649   0.354  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.063   0.838  -0.183  1.00  0.00           C  
HETATM    9  H1  UNL     1      -2.182   1.454  -1.356  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.248   1.791   0.477  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.144  -0.741  -1.047  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.789  -0.335   0.628  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.448   0.040   1.406  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.969  -1.654   1.175  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.562  -2.181  -0.368  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.302  -0.683  -1.253  1.00  0.00           H  
HETATM   17  H9  UNL     1       2.649  -1.260   0.035  1.00  0.00           H  
HETATM   18  H10 UNL     1       1.810  -0.523   1.442  1.00  0.00           H  
HETATM   19  H11 UNL     1       2.655   1.379   0.549  1.00  0.00           H  
HETATM   20  H12 UNL     1       2.566   0.650  -1.149  1.00  0.00           H  
CONECT    1    2    2    2    8
CONECT    2    3
CONECT    3    4    9   10
CONECT    4    5   11   12
CONECT    5    6   13   14
CONECT    6    7   15   16
CONECT    7    8   17   18
CONECT    8   19   20
END
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SMILES for HMDB0250663 (Cyclooctyne)

C1CCCC#CCC1
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INCHI for HMDB0250663 (Cyclooctyne)

InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-6H2
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC8H12
Average Molecular Weight108.184
Monoisotopic Molecular Weight108.093900386
IUPAC Namecyclooctyne
Traditional Namecyclooctyne
CAS Registry NumberNot Available
SMILES
C1CCCC#CCC1
InChI Identifier
InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-6H2
InChI KeyZPWOOKQUDFIEIX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as monocyclic acetylenes. These are monocyclic hydrocarbons containing one or more acetylene groups.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassUnsaturated hydrocarbons
Sub ClassAcetylenes
Direct ParentMonocyclic acetylenes
Alternative Parents
Substituents
  • Monocyclic acetylene
  • Unsaturated aliphatic hydrocarbon
  • 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
logP3.91ALOGPS
logP3.14ChemAxon
logS-3.1ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity36.17 m³·mol⁻¹ChemAxon
Polarizability13.5 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]+125.830932474
DeepCCS[M-H]-123.65530932474
DeepCCS[M-2H]-159.46830932474
DeepCCS[M+Na]+133.97230932474
AllCCS[M+H]+122.932859911
AllCCS[M+H-H2O]+118.032859911
AllCCS[M+NH4]+127.632859911
AllCCS[M+Na]+128.932859911
AllCCS[M-H]-125.732859911
AllCCS[M+Na-2H]-128.332859911
AllCCS[M+HCOO]-131.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
CyclooctyneC1CCCC#CCC11325.4Standard polar33892256
CyclooctyneC1CCCC#CCC1951.6Standard non polar33892256
CyclooctyneC1CCCC#CCC1897.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cyclooctyne GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4i-9400000000-c446ac088319d04fb49b2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cyclooctyne 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 - Cyclooctyne 10V, Positive-QTOFsplash10-0a4i-2900000000-e499606b614c86272ffa2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclooctyne 20V, Positive-QTOFsplash10-0ldi-9200000000-1675fb80eebf75f5a2482021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclooctyne 40V, Positive-QTOFsplash10-0f79-9000000000-478309b7d1c175b4e4422021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclooctyne 10V, Negative-QTOFsplash10-0a4i-0900000000-e16413f7e638bb43ede92021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclooctyne 20V, Negative-QTOFsplash10-0a4i-0900000000-e16413f7e638bb43ede92021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclooctyne 40V, Negative-QTOFsplash10-0a4i-6900000000-aeb3dc168fe48088e9fe2021-10-12Wishart 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 IDNot Available
Chemspider ID120907
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID37815
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 ]