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Showing metabocard for Levulinic acid (HMDB0000720)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:06 UTC
HMDB IDHMDB0000720
Secondary Accession Numbers
  • HMDB00720
Metabolite Identification
Common NameLevulinic acid
DescriptionLevulinic acid, also known as laevulinsaeure or levulate, belongs to the class of organic compounds known as gamma-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the C4 carbon atom. Levulinic acid exists in all living organisms, ranging from bacteria to humans. Levulinic acid is a sweet, acetoin, and acidic tasting compound. Levulinic acid has been detected, but not quantified in, several different foods, such as fruits, green vegetables, chickens (Gallus gallus), root vegetables, and breakfast cereal. This could make levulinic acid a potential biomarker for the consumption of these foods. Levulinic acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Levulinic acid.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000720 (Levulinic acid)

  Mrv1652305271900192D          

  8  7  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   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
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
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3D MOL for HMDB0000720 (Levulinic acid)

HMDB0000720
     RDKit          3D
Levulinic acid
 16 15  0  0  0  0  0  0  0  0999 V2000
   -2.4782    0.6087    0.5722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1102    0.0894    0.8219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7479   -0.0612    1.9636 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2365   -0.2264   -0.3238 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1129   -0.7407    0.0935 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8609    0.2314    0.9207 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4431    1.3633    1.2526 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1179   -0.1542    1.3538 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7495    1.3864    1.3179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5838    1.0844   -0.4222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2483   -0.1877    0.6616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1194    0.7048   -0.9161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7056   -1.0247   -0.9475 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9796   -1.6545    0.7222 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6700   -1.0570   -0.8114 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7952   -0.3621    0.6187 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  8 16  1  0
M  END
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3D SDF for HMDB0000720 (Levulinic acid)

  Mrv1652305271900192D          

  8  7  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   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
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000720

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O3/c1-4(6)2-3-5(7)8/h2-3H2,1H3,(H,7,8)

> <INCHI_KEY>
JOOXCMJARBKPKM-UHFFFAOYSA-N

> <FORMULA>
C5H8O3

> <MOLECULAR_WEIGHT>
116.1152

> <EXACT_MASS>
116.047344122

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
11.226704374068705

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-oxopentanoic acid

> <ALOGPS_LOGP>
-0.14

> <JCHEM_LOGP>
-0.06885744466666677

> <ALOGPS_LOGS>
0.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
19.60659045342587

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.321649025460527

> <JCHEM_PKA_STRONGEST_BASIC>
-7.2827110371620964

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
27.0881

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.39e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
levulinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000720 (Levulinic acid)

HMDB0000720
     RDKit          3D
Levulinic acid
 16 15  0  0  0  0  0  0  0  0999 V2000
   -2.4782    0.6087    0.5722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1102    0.0894    0.8219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7479   -0.0612    1.9636 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2365   -0.2264   -0.3238 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1129   -0.7407    0.0935 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8609    0.2314    0.9207 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4431    1.3633    1.2526 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1179   -0.1542    1.3538 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7495    1.3864    1.3179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5838    1.0844   -0.4222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2483   -0.1877    0.6616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1194    0.7048   -0.9161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7056   -1.0247   -0.9475 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9796   -1.6545    0.7222 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6700   -1.0570   -0.8114 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7952   -0.3621    0.6187 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  8 16  1  0
M  END
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PDB for HMDB0000720 (Levulinic acid)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.976   3.644   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0000720 (Levulinic acid)

COMPND    HMDB0000720
HETATM    1  C1  UNL     1      -2.478   0.609   0.572  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.110   0.089   0.822  1.00  0.00           C  
HETATM    3  O1  UNL     1      -0.748  -0.061   1.964  1.00  0.00           O  
HETATM    4  C3  UNL     1      -0.237  -0.226  -0.324  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.113  -0.741   0.093  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.861   0.231   0.921  1.00  0.00           C  
HETATM    7  O2  UNL     1       1.443   1.363   1.253  1.00  0.00           O  
HETATM    8  O3  UNL     1       3.118  -0.154   1.354  1.00  0.00           O  
HETATM    9  H1  UNL     1      -2.750   1.386   1.318  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.584   1.084  -0.422  1.00  0.00           H  
HETATM   11  H3  UNL     1      -3.248  -0.188   0.662  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.119   0.705  -0.916  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.706  -1.025  -0.947  1.00  0.00           H  
HETATM   14  H6  UNL     1       0.980  -1.655   0.722  1.00  0.00           H  
HETATM   15  H7  UNL     1       1.670  -1.057  -0.811  1.00  0.00           H  
HETATM   16  H8  UNL     1       3.795  -0.362   0.619  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    3    4
CONECT    4    5   12   13
CONECT    5    6   14   15
CONECT    6    7    7    8
CONECT    8   16
END
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SMILES for HMDB0000720 (Levulinic acid)

CC(=O)CCC(O)=O
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INCHI for HMDB0000720 (Levulinic acid)

InChI=1S/C5H8O3/c1-4(6)2-3-5(7)8/h2-3H2,1H3,(H,7,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC5H8O3
Average Molecular Weight116.1152
Monoisotopic Molecular Weight116.047344122
IUPAC Name4-oxopentanoic acid
Traditional Namelevulinic acid
CAS Registry Number123-76-2
SMILES
CC(=O)CCC(O)=O
InChI Identifier
InChI=1S/C5H8O3/c1-4(6)2-3-5(7)8/h2-3H2,1H3,(H,7,8)
InChI KeyJOOXCMJARBKPKM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gamma-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the C4 carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassGamma-keto acids and derivatives
Direct ParentGamma-keto acids and derivatives
Alternative Parents
Substituents
  • Gamma-keto acid
  • Short-chain keto acid
  • Ketone
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Health effectOrganoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Industrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point30 - 33 °CNot Available
Boiling Point245.00 to 246.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility674600 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-0.49HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Neuron
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Attachment loss
  1. Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Missing teeth
  1. Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Periodontal Probing Depth
  1. Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
DrugBank IDDB02239
Phenol Explorer Compound IDNot Available
FooDB IDFDB003296
KNApSAcK IDC00051252
Chemspider ID11091
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkLevulinic_acid
METLIN ID2195
PubChem Compound11579
PDB IDNot Available
ChEBI ID45630
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1016791
References
Synthesis ReferenceCai, Lei; Lu, Xiuyang; He, Long; Xia, Wenli; Ren, Qilong. Review on preparation methods of levulinic acid, a new platform chemical. Xiandai Huagong (2003), 23(4), 14-16.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Lee SH, Kim SO, Chung BC: Gas chromatographic-mass spectrometric determination of urinary oxoacids using O-(2,3,4,5,6-pentafluorobenzyl)oxime-trimethylsilyl ester derivatization and cation-exchange chromatography. J Chromatogr B Biomed Sci Appl. 1998 Nov 20;719(1-2):1-7. [PubMed:9869358 ]
  2. Ohdoi C, Nyhan WL, Kuhara T: Chemical diagnosis of Lesch-Nyhan syndrome using gas chromatography-mass spectrometry detection. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 15;792(1):123-30. [PubMed:12829005 ]
  3. Lopez Montes A, Lorenzo I, Perez Martinez J: [Porphyria and inappropriate antidiuretic hormone syndrome]. Nefrologia. 2004;24 Suppl 3:85-8. [PubMed:15219077 ]
  4. Melgaard B, Clausen J, Rastogi SC: Heavy metal levels and delta-amino-levulinic acid dehydrase levels in peripheral polyneuropathy. Acta Neurol Scand. 1976 Apr;53(4):291-307. [PubMed:178141 ]
  5. Matsui M, Kaji R, Oka N, Nishio T, Kimura J: [Multifocal axonal motor neuropathy associated with anti-ganglioside antibodies]. Rinsho Shinkeigaku. 1992 Oct;32(10):1130-5. [PubMed:1297559 ]
  6. Keithly L, Ferris Wayne G, Cullen DM, Connolly GN: Industry research on the use and effects of levulinic acid: a case study in cigarette additives. Nicotine Tob Res. 2005 Oct;7(5):761-71. [PubMed:16191747 ]
  7. Endo G, Horiguchi S, Kiyota I: Urinary N-acetyl-beta-D-glucosaminidase activity in lead-exposed workers. J Appl Toxicol. 1990 Aug;10(4):235-8. [PubMed:2391405 ]