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Showing metabocard for 3-Methyl-2-butenal (HMDB0012157)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2009-04-06 16:20:10 UTC
Update Date2023-02-21 17:17:42 UTC
HMDB IDHMDB0012157
Secondary Accession Numbers
  • HMDB12157
Metabolite Identification
Common Name3-Methyl-2-butenal
Description3-Methyl-2-butenal, also known as senecialdehyde or 3,3-dimethylacrolein, belongs to the class of organic compounds known as enals. These are alpha,beta-unsaturated aldehydes of the 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-2-butenal has been detected, but not quantified, in several different foods, such as common oregano, beechnuts, oval-leaf huckleberries, tea leaf willows, and red rice. This could make 3-methyl-2-butenal a potential biomarker for the consumption of these foods. 3-Methyl-2-butenal is a derivative of acrolein that is an alpha, beta-unsaturated carbonyl metabolite. It can be formed endogenously during lipid peroxidation or after oxidative stress, and is considered to play an important role in human carcinogenesis. The endogenously formed acroleins are a constant source of DNA damage, can lead to mutation, and can also induce tumours in humans (PMID:8319634 ). 3-Methyl-2-butenal, which is an unsaturated aldehyde bearing substitution at the alkene terminus, is a poor inactivator of the enzymes protein tyrosine phosphatases (PTPs). The inactivation of PTPs can yield profound biological consequences arising from the disruption of cellular signalling pathways (PMID:17655273 ).
Structure
Data?1676999862
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0012157 (3-Methyl-2-butenal)


  Mrv1652309042000342D          

  6  5  0  0  0  0            999 V2000
   -2.6560    1.4839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3705    1.0714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6560    2.3089    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9415    1.0714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2271    1.4839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5126    1.0714    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
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3D MOL for HMDB0012157 (3-Methyl-2-butenal)

HMDB0012157
     RDKit          3D
3-Methyl-2-butenal
 14 13  0  0  0  0  0  0  0  0999 V2000
    0.1365   -0.9655    1.0062 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3079   -0.0245   -0.1166 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6136    0.0332   -0.8034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6559    0.7566   -0.5207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9902    0.7925    0.0766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2027    0.0147    1.0388 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1056   -0.4079    1.9541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6713   -1.7199    0.8040 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0697   -1.5809    1.1544 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9015    1.1247   -0.8303 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3981   -0.5629   -0.2775 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4515   -0.3476   -1.8503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4845    1.4278   -1.3451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7686    1.4597   -0.2902 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  2  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  3 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
M  END
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3D SDF for HMDB0012157 (3-Methyl-2-butenal)


  Mrv1652309042000342D          

  6  5  0  0  0  0            999 V2000
   -2.6560    1.4839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3705    1.0714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6560    2.3089    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9415    1.0714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2271    1.4839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5126    1.0714    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0012157

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CC=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O/c1-5(2)3-4-6/h3-4H,1-2H3

> <INCHI_KEY>
SEPQTYODOKLVSB-UHFFFAOYSA-N

> <FORMULA>
C5H8O

> <MOLECULAR_WEIGHT>
84.1164

> <EXACT_MASS>
84.057514878

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
9.509065212790638

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylbut-2-enal

> <ALOGPS_LOGP>
0.97

> <JCHEM_LOGP>
1.0043273066666667

> <ALOGPS_LOGS>
-0.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-3.9135992021592005

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
26.3215

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.36e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
prenal

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0012157 (3-Methyl-2-butenal)

HMDB0012157
     RDKit          3D
3-Methyl-2-butenal
 14 13  0  0  0  0  0  0  0  0999 V2000
    0.1365   -0.9655    1.0062 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3079   -0.0245   -0.1166 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6136    0.0332   -0.8034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6559    0.7566   -0.5207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9902    0.7925    0.0766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2027    0.0147    1.0388 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1056   -0.4079    1.9541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6713   -1.7199    0.8040 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0697   -1.5809    1.1544 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9015    1.1247   -0.8303 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3981   -0.5629   -0.2775 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4515   -0.3476   -1.8503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4845    1.4278   -1.3451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7686    1.4597   -0.2902 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  2  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  3 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
M  END
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PDB for HMDB0012157 (3-Methyl-2-butenal)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0      -4.958   2.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.292   2.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.958   4.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.624   2.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.291   2.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.957   2.000   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0012157 (3-Methyl-2-butenal)

COMPND    HMDB0012157
HETATM    1  C1  UNL     1       0.136  -0.965   1.006  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.308  -0.024  -0.117  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.614   0.033  -0.803  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.656   0.757  -0.521  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.990   0.793   0.077  1.00  0.00           C  
HETATM    6  O1  UNL     1      -2.203   0.015   1.039  1.00  0.00           O  
HETATM    7  H1  UNL     1      -0.106  -0.408   1.954  1.00  0.00           H  
HETATM    8  H2  UNL     1      -0.671  -1.720   0.804  1.00  0.00           H  
HETATM    9  H3  UNL     1       1.070  -1.581   1.154  1.00  0.00           H  
HETATM   10  H4  UNL     1       1.901   1.125  -0.830  1.00  0.00           H  
HETATM   11  H5  UNL     1       2.398  -0.563  -0.277  1.00  0.00           H  
HETATM   12  H6  UNL     1       1.452  -0.348  -1.850  1.00  0.00           H  
HETATM   13  H7  UNL     1      -0.484   1.428  -1.345  1.00  0.00           H  
HETATM   14  H8  UNL     1      -2.769   1.460  -0.290  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3    4    4
CONECT    3   10   11   12
CONECT    4    5   13
CONECT    5    6    6   14
END
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SMILES for HMDB0012157 (3-Methyl-2-butenal)

CC(C)=CC=O
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INCHI for HMDB0012157 (3-Methyl-2-butenal)

InChI=1S/C5H8O/c1-5(2)3-4-6/h3-4H,1-2H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3,3-Dimethyl-acrylaldehydeChEBI
3,3-DimethylacroleinChEBI
3-MethylcrotonaldehydeChEBI
beta,beta-DimethylacroleinChEBI
beta-MethylcrotonaldehydeChEBI
PrenalChEBI
SenecialdehydeChEBI
SenecioaldehydeChEBI
b,b-DimethylacroleinGenerator
Β,β-dimethylacroleinGenerator
b-MethylcrotonaldehydeGenerator
Β-methylcrotonaldehydeGenerator
3-Methylbut-2-enalHMDB
beta,beta-Dimethylacrylic aldehydeHMDB
2-Methyl-2-buten-4-alHMDB
3,3-DimethylacrylaldehydeHMDB
3-Methyl-2-buten-1-alHMDB
3-Methyl-2-butenalHMDB
3-Methyl-2-butenaldehydeHMDB
β,β-Dimethylacrylic aldehydeHMDB
Chemical FormulaC5H8O
Average Molecular Weight84.1164
Monoisotopic Molecular Weight84.057514878
IUPAC Name3-methylbut-2-enal
Traditional Nameprenal
CAS Registry Number107-86-8
SMILES
CC(C)=CC=O
InChI Identifier
InChI=1S/C5H8O/c1-5(2)3-4-6/h3-4H,1-2H3
InChI KeySEPQTYODOKLVSB-UHFFFAOYSA-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
  • Aldehyde
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point134 °CNot Available
Water Solubility0The Good Scents Company Information System
LogP1.190 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility63.6 g/LALOGPS
logP0.97ALOGPS
logP1ChemAxon
logS-0.12ALOGPS
pKa (Strongest Basic)-3.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity26.32 m³·mol⁻¹ChemAxon
Polarizability9.51 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
DarkChem[M+H]+116.00531661259
DarkChem[M-H]-111.29631661259
DeepCCS[M+H]+121.12430932474
DeepCCS[M-H]-118.64130932474
DeepCCS[M-2H]-154.70930932474
DeepCCS[M+Na]+129.25630932474
AllCCS[M+H]+120.332859911
AllCCS[M+H-H2O]+115.832859911
AllCCS[M+NH4]+124.532859911
AllCCS[M+Na]+125.732859911
AllCCS[M-H]-125.032859911
AllCCS[M+Na-2H]-129.632859911
AllCCS[M+HCOO]-134.732859911

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, 2022.3.33 minutes32390414
Predicted by Siyang on May 30, 202210.2265 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.35 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1395.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid369.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid138.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid246.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid54.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid335.3 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 Acid438.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)119.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid760.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid306.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid847.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid277.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid274.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate462.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA378.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water79.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-Methyl-2-butenalCC(C)=CC=O1098.1Standard polar33892256
3-Methyl-2-butenalCC(C)=CC=O707.7Standard non polar33892256
3-Methyl-2-butenalCC(C)=CC=O762.1Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Campylobacter jejuni infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Clostridium difficile infection		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Nonalcoholic fatty liver disease (NAFLD)		 details
Associated Disorders and Diseases
Disease References
Nonalcoholic fatty liver disease
  1. Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP, Rioux KP: Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol. 2013 Jul;11(7):868-75.e1-3. doi: 10.1016/j.cgh.2013.02.015. Epub 2013 Feb 27. [PubMed:23454028 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008134
KNApSAcK IDC00052688
Chemspider ID54980
KEGG Compound IDC15604
BioCyc IDPRENAL
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound61020
PDB IDNot Available
ChEBI ID15825
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1037231
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Eder E, Hoffman C, Sporer S, Scheckenbach S: Biomonitoring studies and susceptibility markers for acrolein congeners and allylic and benzyl compounds. Environ Health Perspect. 1993 Mar;99:245-7. [PubMed:8319634 ]
  2. Seiner DR, LaButti JN, Gates KS: Kinetics and mechanism of protein tyrosine phosphatase 1B inactivation by acrolein. Chem Res Toxicol. 2007 Sep;20(9):1315-20. Epub 2007 Jul 27. [PubMed:17655273 ]

Enzymes

Enzyme Details
1. Carbonyl reductase [NADPH] 1
General function:
Involved in oxidoreductase activity
Specific function:
NADPH-dependent reductase with broad substrate specificity. Catalyzes the reduction of a wide variety of carbonyl compounds including quinones, prostaglandins, menadione, plus various xenobiotics. Catalyzes the reduction of the antitumor anthracyclines doxorubicin and daunorubicin to the cardiotoxic compounds doxorubicinol and daunorubicinol. Can convert prostaglandin E2 to prostaglandin F2-alpha. Can bind glutathione, which explains its higher affinity for glutathione-conjugated substrates. Catalyzes the reduction of S-nitrosoglutathione.
Gene Name:
CBR1
Uniprot ID:
P16152
Molecular weight:
30374.73
Reactions
3-Methyl-2-butenal → Prenoldetails