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Showing metabocard for 3-methyl-4-cis-hydroxy-2-butenal (HMDB0304139)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 07:30:15 UTC
Update Date2021-09-24 07:30:15 UTC
HMDB IDHMDB0304139
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-methyl-4-cis-hydroxy-2-butenal
Description3-methyl-4-cis-hydroxy-2-butenal, also known as (Z)-4-hydroxy-3-methyl-2-butenal, is a member of the class of compounds known as enals. Enals are an alpha,beta-unsaturated aldehyde of general formula RC=C-CH=O in which the aldehydic C=O function is conjugated to a C=C triple bond at the alpha,beta position. 3-methyl-4-cis-hydroxy-2-butenal is soluble (in water) and an extremely weak acidic compound (based on its pKa). 3-methyl-4-cis-hydroxy-2-butenal can be found in a number of food items such as fennel, sorrel, savoy cabbage, and hickory nut, which makes 3-methyl-4-cis-hydroxy-2-butenal a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304139 (3-methyl-4-cis-hydroxy-2-butenal)


  Mrv1652303082006182D          

  8  7  0  0  0  0            999 V2000
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    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 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
    2.0625   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  2  2  0  0  0  0
  5  4  1  0  0  0  0
  6  3  2  0  0  0  0
  7  4  1  0  0  0  0
  8  2  1  0  0  0  0
M  END
Download

3D MOL for HMDB0304139 (3-methyl-4-cis-hydroxy-2-butenal)

HMDB0304139
     RDKit          3D
3-methyl-4-cis-hydroxy-2-butenal
 15 14  0  0  0  0  0  0  0  0999 V2000
   -1.2874   -1.3154   -0.2849 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1941   -0.3212    0.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0193   -0.6984   -0.2249 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1853    0.1044    0.0107 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3117   -0.3497   -0.2749 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4971    0.9760    0.6165 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3341    1.7408   -0.2324 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9811   -1.9339   -1.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4700   -1.8825    0.6540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1912   -0.7025   -0.5460 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1983   -1.6973   -0.6589 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1075    1.0802    0.4243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1660    0.7626    1.5175 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3195    1.5587    1.0311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0206    2.6781   -0.1328 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  2  6  1  0
  6  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
M  END
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3D SDF for HMDB0304139 (3-methyl-4-cis-hydroxy-2-butenal)


  Mrv1652303082006182D          

  8  7  0  0  0  0            999 V2000
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    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 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
    2.0625   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  2  2  0  0  0  0
  5  4  1  0  0  0  0
  6  3  2  0  0  0  0
  7  4  1  0  0  0  0
  8  2  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304139

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]\C(C=O)=C(/C)CO

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O2/c1-5(4-7)2-3-6/h2-3,7H,4H2,1H3/b5-2-

> <INCHI_KEY>
BSHDRMLUCYMQOP-DJWKRKHSSA-N

> <FORMULA>
C5H8O2

> <MOLECULAR_WEIGHT>
100.117

> <EXACT_MASS>
100.052429498

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.374585171848707

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2Z)-4-hydroxy-3-methylbut-2-enal

> <ALOGPS_LOGP>
-0.34

> <JCHEM_LOGP>
-0.2764438500000001

> <ALOGPS_LOGS>
0.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.12188716033462

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7454865560696353

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
28.0962

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.59e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2Z)-4-hydroxy-3-methylbut-2-enal

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0304139 (3-methyl-4-cis-hydroxy-2-butenal)

HMDB0304139
     RDKit          3D
3-methyl-4-cis-hydroxy-2-butenal
 15 14  0  0  0  0  0  0  0  0999 V2000
   -1.2874   -1.3154   -0.2849 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1941   -0.3212    0.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0193   -0.6984   -0.2249 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1853    0.1044    0.0107 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3117   -0.3497   -0.2749 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4971    0.9760    0.6165 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3341    1.7408   -0.2324 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9811   -1.9339   -1.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4700   -1.8825    0.6540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1912   -0.7025   -0.5460 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1983   -1.6973   -0.6589 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1075    1.0802    0.4243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1660    0.7626    1.5175 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3195    1.5587    1.0311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0206    2.6781   -0.1328 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  2  6  1  0
  6  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
M  END
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PDB for HMDB0304139 (3-methyl-4-cis-hydroxy-2-butenal)

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   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  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.850  -1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000  -2.667   0.000  0.00  0.00           O+0
HETATM    8  H   UNK     0       2.310   1.334   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    3    5    8                                                  
CONECT    3    2    6                                                       
CONECT    4    5    7                                                       
CONECT    5    1    2    4                                                  
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    2                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0304139 (3-methyl-4-cis-hydroxy-2-butenal)

COMPND    HMDB0304139
HETATM    1  C1  UNL     1      -1.287  -1.315  -0.285  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.194  -0.321   0.038  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.019  -0.698  -0.225  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.185   0.104   0.011  1.00  0.00           C  
HETATM    5  O1  UNL     1       3.312  -0.350  -0.275  1.00  0.00           O  
HETATM    6  C5  UNL     1      -0.497   0.976   0.617  1.00  0.00           C  
HETATM    7  O2  UNL     1      -1.334   1.741  -0.232  1.00  0.00           O  
HETATM    8  H1  UNL     1      -0.981  -1.934  -1.132  1.00  0.00           H  
HETATM    9  H2  UNL     1      -1.470  -1.883   0.654  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.191  -0.703  -0.546  1.00  0.00           H  
HETATM   11  H4  UNL     1       1.198  -1.697  -0.659  1.00  0.00           H  
HETATM   12  H5  UNL     1       2.107   1.080   0.424  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.166   0.763   1.517  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.320   1.559   1.031  1.00  0.00           H  
HETATM   15  H8  UNL     1      -1.021   2.678  -0.133  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    3    6
CONECT    3    4   11
CONECT    4    5    5   12
CONECT    6    7   13   14
CONECT    7   15
END
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SMILES for HMDB0304139 (3-methyl-4-cis-hydroxy-2-butenal)

[H]\C(C=O)=C(/C)CO
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INCHI for HMDB0304139 (3-methyl-4-cis-hydroxy-2-butenal)

InChI=1S/C5H8O2/c1-5(4-7)2-3-6/h2-3,7H,4H2,1H3/b5-2-
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(Z)-4-Hydroxy-3-methyl-2-butenalChEBI
Chemical FormulaC5H8O2
Average Molecular Weight100.117
Monoisotopic Molecular Weight100.052429498
IUPAC Name(2Z)-4-hydroxy-3-methylbut-2-enal
Traditional Name(2Z)-4-hydroxy-3-methylbut-2-enal
CAS Registry NumberNot Available
SMILES
[H]\C(C=O)=C(/C)CO
InChI Identifier
InChI=1S/C5H8O2/c1-5(4-7)2-3-6/h2-3,7H,4H2,1H3/b5-2-
InChI KeyBSHDRMLUCYMQOP-DJWKRKHSSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as enals. These are an alpha,beta-unsaturated aldehyde of general formula RC=C-CH=O in which the aldehydic C=O function is conjugated to a C=C triple bond at the alpha,beta position.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentEnals
Alternative Parents
Substituents
  • Enal
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Primary alcohol
  • Aldehyde
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
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
logP-0.34ALOGPS
logP-0.28ChemAxon
logS0.2ALOGPS
pKa (Strongest Acidic)15.12ChemAxon
pKa (Strongest Basic)-2.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity28.1 m³·mol⁻¹ChemAxon
Polarizability10.37 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
AllCCS[M+H]+124.96732859911
AllCCS[M+H-H2O]+120.60132859911
AllCCS[M+Na]+130.21732859911
AllCCS[M+NH4]+129.04132859911
AllCCS[M-H]-125.45132859911
AllCCS[M+Na-2H]-129.32732859911
AllCCS[M+HCOO]-133.60532859911
DeepCCS[M+H]+125.09430932474
DeepCCS[M-H]-122.58930932474
DeepCCS[M-2H]-158.66530932474
DeepCCS[M+Na]+133.57430932474

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal GC-MS (TMS_1_1) - 70eV, PositiveNot Available2022-08-08Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal 10V, Positive-QTOFsplash10-0f89-9500000000-049c62af9d498331a0f12019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal 20V, Positive-QTOFsplash10-001l-9000000000-afef61b5422163c44dcb2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal 40V, Positive-QTOFsplash10-05n3-9000000000-4259ffbcd4aae8be937c2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal 10V, Negative-QTOFsplash10-0002-9000000000-527b7f02c93c291dda332019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal 20V, Negative-QTOFsplash10-00dj-9000000000-e139a08814f79c97039b2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal 40V, Negative-QTOFsplash10-05mo-9000000000-4e6fa4240c558d172f972019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal 10V, Positive-QTOFsplash10-0536-9000000000-3375d01eeacc68cdfba12021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal 20V, Positive-QTOFsplash10-0006-9000000000-076f86ec2b20c21dce812021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal 40V, Positive-QTOFsplash10-0fr6-9000000000-a0486c18973c6d6403472021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal 10V, Negative-QTOFsplash10-001i-9000000000-062ea9d9ce885765b1ff2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal 20V, Negative-QTOFsplash10-0159-9000000000-1cb55f18ad02fbc4ac6b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-methyl-4-cis-hydroxy-2-butenal 40V, Negative-QTOFsplash10-00kf-9000000000-72cffa74f0bec6b5d36f2021-10-21Wishart 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 IDFDB030442
KNApSAcK IDNot Available
Chemspider ID14441281
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12487266
PDB IDNot Available
ChEBI ID133364
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 ReferencesNot Available