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Showing metabocard for cis-3-Chloro-2-propene-1-ol (HMDB0060456)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 01:22:07 UTC
Update Date2023-02-21 17:30:00 UTC
HMDB IDHMDB0060456
Secondary Accession Numbers
  • HMDB60456
Metabolite Identification
Common Namecis-3-Chloro-2-propene-1-ol
Descriptioncis-3-Chloro-2-propene-1-ol, also known as cis-3-chloroallyl alcohol, belongs to the class of organic compounds known as vinyl chlorides. These are vinyl halides in which a chlorine atom is bonded to an sp2-hybridised carbon atom. These are compounds comprising the primary alcohol functional group, with the general strucuture RCOH (R=alkyl, aryl). cis-3-Chloro-2-propene-1-ol is an extremely weak basic (essentially neutral) compound (based on its pKa). cis-3-Chloro-2-propene-1-ol exists in all living organisms, ranging from bacteria to humans.
Structure
Data?1677000600
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060456 (cis-3-Chloro-2-propene-1-ol)


  Mrv0541 05161318222D          

  5  4  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
M  END
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3D MOL for HMDB0060456 (cis-3-Chloro-2-propene-1-ol)

HMDB0060456
     RDKit          3D
cis-3-Chloro-2-propene-1-ol
 10  9  0  0  0  0  0  0  0  0999 V2000
   -1.4519    0.3772   -1.1703 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8719    0.0692    0.0727 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4840   -0.4616   -0.1171 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5565    0.1305    0.4046 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3953    1.5904    1.3543 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.0135   -0.3980   -1.4357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5137   -0.6530    0.6124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8016    0.9802    0.7159 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6637   -1.3627   -0.6936 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5531   -0.2722    0.2568 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  1  6  1  0
  2  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
M  END
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3D SDF for HMDB0060456 (cis-3-Chloro-2-propene-1-ol)


  Mrv0541 05161318222D          

  5  4  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060456

> <DATABASE_NAME>
hmdb

> <SMILES>
OC\C=C/Cl

> <INCHI_IDENTIFIER>
InChI=1S/C3H5ClO/c4-2-1-3-5/h1-2,5H,3H2/b2-1-

> <INCHI_KEY>
HJGHXDNIPAWLLE-UPHRSURJSA-N

> <FORMULA>
C3H5ClO

> <MOLECULAR_WEIGHT>
92.524

> <EXACT_MASS>
92.002892489

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
8.394140434873673

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2Z)-3-chloroprop-2-en-1-ol

> <ALOGPS_LOGP>
0.52

> <JCHEM_LOGP>
0.5298702816666665

> <ALOGPS_LOGS>
0.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.57758243866936

> <JCHEM_PKA_STRONGEST_BASIC>
-2.5461654413260213

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
22.2256

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.67e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cis-3-chloroallyl alcohol

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0060456 (cis-3-Chloro-2-propene-1-ol)

HMDB0060456
     RDKit          3D
cis-3-Chloro-2-propene-1-ol
 10  9  0  0  0  0  0  0  0  0999 V2000
   -1.4519    0.3772   -1.1703 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8719    0.0692    0.0727 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4840   -0.4616   -0.1171 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5565    0.1305    0.4046 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3953    1.5904    1.3543 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.0135   -0.3980   -1.4357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5137   -0.6530    0.6124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8016    0.9802    0.7159 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6637   -1.3627   -0.6936 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5531   -0.2722    0.2568 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  1  6  1  0
  2  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
M  END
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PDB for HMDB0060456 (cis-3-Chloro-2-propene-1-ol)

HEADER    PROTEIN                                 16-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-13         0                                  
HETATM    1  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4 Cl   UNK     0      -0.770  -1.334   0.000  0.00  0.00          Cl+0
HETATM    5  O   UNK     0       3.850  -1.334   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2                                                            
CONECT    5    3                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for HMDB0060456 (cis-3-Chloro-2-propene-1-ol)

COMPND    HMDB0060456
HETATM    1  O1  UNL     1      -1.452   0.377  -1.170  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.872   0.069   0.073  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.484  -0.462  -0.117  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.557   0.130   0.405  1.00  0.00           C  
HETATM    5 CL1  UNL     1       1.395   1.590   1.354  1.00  0.00          CL  
HETATM    6  H1  UNL     1      -2.013  -0.398  -1.436  1.00  0.00           H  
HETATM    7  H2  UNL     1      -1.514  -0.653   0.612  1.00  0.00           H  
HETATM    8  H3  UNL     1      -0.802   0.980   0.716  1.00  0.00           H  
HETATM    9  H4  UNL     1       0.664  -1.363  -0.694  1.00  0.00           H  
HETATM   10  H5  UNL     1       2.553  -0.272   0.257  1.00  0.00           H  
CONECT    1    2    6
CONECT    2    3    7    8
CONECT    3    4    4    9
CONECT    4    5   10
END
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SMILES for HMDB0060456 (cis-3-Chloro-2-propene-1-ol)

OC\C=C/Cl
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INCHI for HMDB0060456 (cis-3-Chloro-2-propene-1-ol)

InChI=1S/C3H5ClO/c4-2-1-3-5/h1-2,5H,3H2/b2-1-
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View in JSmolView Stereo Labels
Synonyms
ValueSource
cis-3-Chloroallyl alcoholChEBI
cis-3-chloro-2-Propene-1-olChEBI
Chemical FormulaC3H5ClO
Average Molecular Weight92.524
Monoisotopic Molecular Weight92.002892489
IUPAC Name(2Z)-3-chloroprop-2-en-1-ol
Traditional Namecis-3-chloroallyl alcohol
CAS Registry NumberNot Available
SMILES
OC\C=C/Cl
InChI Identifier
InChI=1S/C3H5ClO/c4-2-1-3-5/h1-2,5H,3H2/b2-1-
InChI KeyHJGHXDNIPAWLLE-UPHRSURJSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as vinyl chlorides. These are vinyl halides in which a chlorine atom is bonded to an sp2-hybridised carbon atom.
KingdomOrganic compounds
Super ClassOrganohalogen compounds
ClassVinyl halides
Sub ClassVinyl chlorides
Direct ParentVinyl chlorides
Alternative Parents
Substituents
  • Chloroalkene
  • Haloalkene
  • Vinyl chloride
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organochloride
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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
Water Solubility167 g/LALOGPS
logP0.52ALOGPS
logP0.53ChemAxon
logS0.26ALOGPS
pKa (Strongest Acidic)15.58ChemAxon
pKa (Strongest Basic)-2.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity22.23 m³·mol⁻¹ChemAxon
Polarizability8.39 ųChemAxon
Number of Rings0ChemAxon
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]+119.50330932474
DeepCCS[M-H]-117.60830932474
DeepCCS[M-2H]-152.86830932474
DeepCCS[M+Na]+127.13930932474
AllCCS[M+H]+125.032859911
AllCCS[M+H-H2O]+120.632859911
AllCCS[M+NH4]+129.132859911
AllCCS[M+Na]+130.332859911
AllCCS[M-H]-137.632859911
AllCCS[M+Na-2H]-143.232859911
AllCCS[M+HCOO]-149.332859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.2.83 minutes32390414
Predicted by Siyang on May 30, 20229.7931 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.96 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid806.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid339.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid100.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid250.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid64.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid270.1 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 Acid305.2 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)250.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid593.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid52.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid870.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid220.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid264.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate633.2 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA253.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water196.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
cis-3-Chloro-2-propene-1-olOC\C=C/Cl1582.1Standard polar33892256
cis-3-Chloro-2-propene-1-olOC\C=C/Cl725.9Standard non polar33892256
cis-3-Chloro-2-propene-1-olOC\C=C/Cl747.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
cis-3-Chloro-2-propene-1-ol,1TMS,isomer #1C[Si](C)(C)OC/C=C\Cl933.1Semi standard non polar33892256
cis-3-Chloro-2-propene-1-ol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC/C=C\Cl1130.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - cis-3-Chloro-2-propene-1-ol GC-MS (Non-derivatized) - 70eV, Positivesplash10-055f-9000000000-a67937e76a9ac12ca31d2017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - cis-3-Chloro-2-propene-1-ol GC-MS (1 TMS) - 70eV, Positivesplash10-00fr-9300000000-04b75f98817983db1ad52017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - cis-3-Chloro-2-propene-1-ol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - cis-3-Chloro-2-propene-1-ol 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 - cis-3-Chloro-2-propene-1-ol 10V, Positive-QTOFsplash10-00dl-9000000000-7790483b5c20d83bd0412017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cis-3-Chloro-2-propene-1-ol 20V, Positive-QTOFsplash10-00di-9000000000-7b77153318317174b3802017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cis-3-Chloro-2-propene-1-ol 40V, Positive-QTOFsplash10-05g0-9000000000-b8967b7eba1a7ed39a642017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cis-3-Chloro-2-propene-1-ol 10V, Negative-QTOFsplash10-0006-9000000000-b3d9dcda6d8b2af8d51a2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cis-3-Chloro-2-propene-1-ol 20V, Negative-QTOFsplash10-0006-9000000000-4c69270906e92591d1652017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cis-3-Chloro-2-propene-1-ol 40V, Negative-QTOFsplash10-0a4i-9000000000-5f2e33e968b383753e372017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cis-3-Chloro-2-propene-1-ol 10V, Positive-QTOFsplash10-00di-9000000000-7cc274da6d5f357c12982021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cis-3-Chloro-2-propene-1-ol 20V, Positive-QTOFsplash10-022c-9000000000-8075d45c323182c3fc0a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cis-3-Chloro-2-propene-1-ol 40V, Positive-QTOFsplash10-000i-9000000000-e6cae368b176706adf4b2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cis-3-Chloro-2-propene-1-ol 10V, Negative-QTOFsplash10-001i-9000000000-c2fa753da65a4bac80a12021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cis-3-Chloro-2-propene-1-ol 20V, Negative-QTOFsplash10-001i-9000000000-c2fa753da65a4bac80a12021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cis-3-Chloro-2-propene-1-ol 40V, Negative-QTOFsplash10-001i-9000000000-c2fa753da65a4bac80a12021-10-12Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
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 IDNot Available
KEGG Compound IDC06612
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound643775
PDB IDNot Available
ChEBI ID28967
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. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

Enzymes

Enzyme Details
1. Alcohol dehydrogenase class-3
General function:
Involved in zinc ion binding
Specific function:
Class-III ADH is remarkably ineffective in oxidizing ethanol, but it readily catalyzes the oxidation of long-chain primary alcohols and the oxidation of S-(hydroxymethyl) glutathione.
Gene Name:
ADH5
Uniprot ID:
P11766
Molecular weight:
39723.945
Reactions
cis-3-Chloro-2-propene-1-ol + NAD → cis-3-Chloroallyl aldehyde + NADH + Hydrogen Iondetails