MiMeDB: Showing metabocard for Limonene (MMDBc0033666)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:58:07 UTC

Update Date

2024-04-20 06:12:49 UTC

Metabolite ID

MMDBc0033666

Metabolite Identification

Common Name

Limonene

Description

L-lactaldehyde is an intermediate metabolite in the pyruvate metabolism pathway. L-lactaldehyde is irreversibly produced from pyruvaldehyde via the enzyme aldehyde reductase (EC:1.1.1.21) which is then irreversibly converted to propylene glycol via aldehyde reductase (EC:1.1.1.21).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241223232D          

 15 16  0  0  0  0            999 V2000
   -1.3921   -3.2303    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6776   -3.6428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6776   -4.4678    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0369   -3.2303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7513   -3.6428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4658   -3.2303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1803   -3.6428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9340   -3.3072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1889   -2.5226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9959   -2.3511    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5479   -2.9642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2930   -3.7488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4860   -3.9203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0735   -4.6348    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2665   -4.4633    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  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
  7  8  4  0  0  0  0
  8  9  4  0  0  0  0
  9 10  4  0  0  0  0
 10 11  4  0  0  0  0
 11 12  4  0  0  0  0
 12 13  4  0  0  0  0
  8 13  4  0  0  0  0
 13 14  4  0  0  0  0
 14 15  4  0  0  0  0
  7 15  4  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033666

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)CCCc1cnc2ccccc12

> <INCHI_IDENTIFIER>
InChI=1S/C12H12NO2/c14-12(15)7-3-4-9-8-13-11-6-2-1-5-10(9)11/h1-2,5-6,8H,3-4,7H2,(H,14,15)

> <INCHI_KEY>
LVZHFCNXDNVHJI-UHFFFAOYSA-N

> <FORMULA>
C12H12NO2

> <MOLECULAR_WEIGHT>
202.2292

> <EXACT_MASS>
202.086803633

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
21.596033812149344

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-(indol-3-yl)butanoic acid

> <ALOGPS_LOGP>
2.38

> <JCHEM_LOGP>
1.364417777934613

> <ALOGPS_LOGS>
-2.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.390382003380385

> <JCHEM_PKA_STRONGEST_BASIC>
5.2602285422046196

> <JCHEM_POLAR_SURFACE_AREA>
50.19

> <JCHEM_REFRACTIVITY>
56.145900000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.56e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-indolebutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      -2.599  -6.030   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.265  -6.800   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.265  -8.340   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.069  -6.030   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.402  -6.800   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.736  -6.030   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.070  -6.800   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.477  -6.173   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.953  -4.709   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.459  -4.389   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.489  -5.533   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.014  -6.998   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.507  -7.318   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       5.737  -8.652   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       4.231  -8.331   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   15                                                  
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    8   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14    7                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

Synonyms

Not Available

Molecular Formula

C₁₂H₁₂NO₂

Average Mass

202.2292

Monoisotopic Mass

202.086803633

IUPAC Name

4-(indol-3-yl)butanoic acid

Traditional Name

3-indolebutyric acid

CAS Registry Number

598-35-6

SMILES

OC(=O)CCCc1cnc2ccccc12

InChI Identifier

InChI=1S/C12H12NO2/c14-12(15)7-3-4-9-8-13-11-6-2-1-5-10(9)11/h1-2,5-6,8H,3-4,7H2,(H,14,15)

InChI Key

LVZHFCNXDNVHJI-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

3-alkylindoles

Alternative Parents

Substituents

3-alkylindole
Substituted pyrrole
Benzenoid
Pyrrole
Heteroaromatic compound
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Azacycle
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxide
Carbonyl group
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.36 g/L	ALOGPS
logP	2.38	ALOGPS
logP	1.36	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	4.39	ChemAxon
pKa (Strongest Basic)	5.26	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	50.19 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	56.15 m³·mol⁻¹	ChemAxon
Polarizability	21.6 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Mitochondria

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	3	Human feces; Human saliva	Unknown
Bacteria	Proteobacteria	58	Human ; Human feces
Archaea/Archaea	Euryarchaeota	6
Bacteria	Firmicutes	10	Human ; Human feces; Catfish
Bacteria	Bacteroidetes	1	Human ; Human feces

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Limonene

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Akhy MT, Brown CM, Old DC: L-Rhamnose utilisation in Salmonella typhimurium. J Appl Bacteriol. 1984 Apr;56(2):269-74. doi: 10.1111/j.1365-2672.1984.tb01347.x. [PubMed:6373710 ]
Chen YM, Chakrabarti T, Lin EC: Constitutive activation of L-fucose genes by an unlinked mutation in Escherichia coli. J Bacteriol. 1984 Aug;159(2):725-9. doi: 10.1128/jb.159.2.725-729.1984. [PubMed:6378890 ]
Chen YM, Lin EC: Dual control of a common L-1,2-propanediol oxidoreductase by L-fucose and L-rhamnose in Escherichia coli. J Bacteriol. 1984 Mar;157(3):828-32. doi: 10.1128/jb.157.3.828-832.1984. [PubMed:6421801 ]
Ros J, Aguilar J: Genetic and structural evidence for the presence of propanediol oxidoreductase isoenzymes in Escherichia coli. J Gen Microbiol. 1984 Mar;130(3):687-92. doi: 10.1099/00221287-130-3-687. [PubMed:6427403 ]
Casazza JP, Felver ME, Veech RL: The metabolism of acetone in rat. J Biol Chem. 1984 Jan 10;259(1):231-6. [PubMed:6706932 ]
ENGLESBERG E: Physiological basis for rhamnose utilization by a mutant of Pasteurella pestis. I. Experiments with resting cells; the isolation of lactic aldehyde. J Bacteriol. 1957 Jul;74(1):8-11. doi: 10.1128/jb.74.1.8-11.1957. [PubMed:13462953 ]
SANDMAN RP, MILLER ON: Studies on the metabolism of lactaldehyde. I. Separation and determination of lactaldehyde and related 3-carbon compounds. J Biol Chem. 1958 Jan;230(1):353-9. [PubMed:13502404 ]
TING SM, SELLINGER OZ, MILLER ON: THE METABOLISM OF LACTALDEHYDE. VI. THE REDUCTION OF D- AND L-LACTALDEHYDE IN RAT LIVER. Biochim Biophys Acta. 1964 Aug 26;89:217-25. doi: 10.1016/0926-6569(64)90210-x. [PubMed:14203169 ]
TING SM, MILLER ON, SELLINGER OZ: THE METABOLISM OF LACTALDEHYDE. VII. THE OXIDATION OF D-LACTALDEHYDE IN RAT LIVER. Biochim Biophys Acta. 1965 Mar 8;97:407-15. doi: 10.1016/0304-4165(65)90151-0. [PubMed:14323585 ]
Di Costanzo L, Gomez GA, Christianson DW: Crystal structure of lactaldehyde dehydrogenase from Escherichia coli and inferences regarding substrate and cofactor specificity. J Mol Biol. 2007 Feb 16;366(2):481-93. doi: 10.1016/j.jmb.2006.11.023. Epub 2006 Nov 10. [PubMed:17173928 ]

Showing metabocard for Limonene (MMDBc0033666)

MOL for #<Metabolite:0x00007fece75e0a48>

3D MOL for #<Metabolite:0x00007fece75e0a48>

3D SDF for #<Metabolite:0x00007fece75e0a48>

3D-SDF for #<Metabolite:0x00007fece75e0a48>

PDB for #<Metabolite:0x00007fece75e0a48>

3D PDB for #<Metabolite:0x00007fece75e0a48>

SMILES for #<Metabolite:0x00007fece75e0a48>

INCHI for #<Metabolite:0x00007fece75e0a48>

Structure for #<Metabolite:0x00007fece75e0a48>

3D Structure for #<Metabolite:0x00007fece75e0a48>