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Showing metabocard for Imidazoleacetic acid (HMDB0002024)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:32 UTC
Update Date2023-02-21 17:16:04 UTC
HMDB IDHMDB0002024
Secondary Accession Numbers
  • HMDB0060261
  • HMDB02024
  • HMDB60261
Metabolite Identification
Common NameImidazoleacetic acid
DescriptionImidazol-4-ylacetic acid is a monocarboxylic acid that is acetic acid in which one of the methyl hydrogens has been replaced by an imidazol-4-yl group. It has a role as a mouse metabolite. It is a monocarboxylic acid and a member of imidazoles. It derives from an acetic acid. It is a conjugate acid of an imidazol-4-ylacetate. It is a tautomer of an imidazol-5-ylacetic acid and a 2H-imidazol-4-ylacetic acid. Imidazoleacetic acid, also known as 4(5)-imidazoleacetate or IAA, belongs to the class of organic compounds known as imidazolyl carboxylic acids and derivatives. These are organic compounds containing a carboxylic acid chain (of at least 2 carbon atoms) linked to an imidazole ring. Imidazoleacetic acid exists in all living organisms, ranging from bacteria to humans. imidazoleacetic acid can be biosynthesized from imidazole-4-acetaldehyde through its interaction with the enzyme aldehyde dehydrogenase, mitochondrial. In humans, imidazoleacetic acid is involved in histidine metabolism. Outside of the human body, Imidazoleacetic acid has been detected, but not quantified in several different foods, such as chinese cinnamons, jostaberries, vanilla, butternut squash, and red rices. Imidazoleacetic acid is a potentially toxic compound. Imidazoleacetic acid is a metabolite product of Histamine metabolism.
Structure
Data?1676999764
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002024 (Imidazoleacetic acid)

  Mrv1652305271900162D          

  9  9  0  0  0  0            999 V2000
   19.3428   -4.0814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.3866   -3.0196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4930   -4.6085    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.0805   -3.3391    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.1604   -4.1236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9451   -4.3786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9055   -3.3391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8255   -4.1236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5581   -3.8265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2  9  2  0  0  0  0
  3  5  1  0  0  0  0
  3  8  1  0  0  0  0
  4  7  1  0  0  0  0
  4  8  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  6  9  1  0  0  0  0
M  END
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3D MOL for HMDB0002024 (Imidazoleacetic acid)

HMDB0002024
     RDKit          3D
Imidazoleacetic acid
 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.1351    0.7461   -1.4990 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9127    0.0057   -0.4828 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4810   -1.2315   -0.3486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9874    0.5283    0.5645 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4225    0.3208    0.1066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0925    1.0180   -0.8615 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3360    0.4868   -0.9258 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4186   -0.5171   -0.0159 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2626   -0.6398    0.6329 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7052   -1.7410    0.5090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1798   -0.0335    1.4881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1159    1.6203    0.7436 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7033    1.8358   -1.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3145   -1.1320    0.1784 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9672   -1.2672    1.3871 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9  5  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  6 13  1  0
  8 14  1  0
  9 15  1  0
M  END
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3D SDF for HMDB0002024 (Imidazoleacetic acid)

  Mrv1652305271900162D          

  9  9  0  0  0  0            999 V2000
   19.3428   -4.0814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.3866   -3.0196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4930   -4.6085    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.0805   -3.3391    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.1604   -4.1236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9451   -4.3786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9055   -3.3391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8255   -4.1236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5581   -3.8265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2  9  2  0  0  0  0
  3  5  1  0  0  0  0
  3  8  1  0  0  0  0
  4  7  1  0  0  0  0
  4  8  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  6  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002024

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CC1=CN=CN1

> <INCHI_IDENTIFIER>
InChI=1S/C5H6N2O2/c8-5(9)1-4-2-6-3-7-4/h2-3H,1H2,(H,6,7)(H,8,9)

> <INCHI_KEY>
PRJKNHOMHKJCEJ-UHFFFAOYSA-N

> <FORMULA>
C5H6N2O2

> <MOLECULAR_WEIGHT>
126.1133

> <EXACT_MASS>
126.042927446

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.472699109880597

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(1H-imidazol-5-yl)acetic acid

> <ALOGPS_LOGP>
-0.50

> <JCHEM_LOGP>
-1.3990613301983859

> <ALOGPS_LOGS>
-0.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.995890284546483

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6538030747064596

> <JCHEM_PKA_STRONGEST_BASIC>
6.776708441179222

> <JCHEM_POLAR_SURFACE_AREA>
65.97999999999999

> <JCHEM_REFRACTIVITY>
30.197899999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.33e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
IMAC

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0002024 (Imidazoleacetic acid)

HMDB0002024
     RDKit          3D
Imidazoleacetic acid
 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.1351    0.7461   -1.4990 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9127    0.0057   -0.4828 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4810   -1.2315   -0.3486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9874    0.5283    0.5645 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4225    0.3208    0.1066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0925    1.0180   -0.8615 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3360    0.4868   -0.9258 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4186   -0.5171   -0.0159 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2626   -0.6398    0.6329 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7052   -1.7410    0.5090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1798   -0.0335    1.4881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1159    1.6203    0.7436 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7033    1.8358   -1.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3145   -1.1320    0.1784 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9672   -1.2672    1.3871 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9  5  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  6 13  1  0
  8 14  1  0
  9 15  1  0
M  END
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PDB for HMDB0002024 (Imidazoleacetic 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  O   UNK     0      36.107  -7.619   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      34.322  -5.637   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0      30.787  -8.603   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0      30.017  -6.233   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      32.033  -7.697   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      33.498  -8.173   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      31.557  -6.233   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      29.541  -7.697   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      34.642  -7.143   0.000  0.00  0.00           C+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3    5    8                                                       
CONECT    4    7    8                                                       
CONECT    5    3    6    7                                                  
CONECT    6    5    9                                                       
CONECT    7    4    5                                                       
CONECT    8    3    4                                                       
CONECT    9    1    2    6                                                  
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0002024 (Imidazoleacetic acid)

COMPND    HMDB0002024
HETATM    1  O1  UNL     1      -2.135   0.746  -1.499  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.913   0.006  -0.483  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.481  -1.231  -0.349  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.987   0.528   0.564  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.423   0.321   0.107  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.092   1.018  -0.861  1.00  0.00           C  
HETATM    7  N1  UNL     1       2.336   0.487  -0.926  1.00  0.00           N  
HETATM    8  C5  UNL     1       2.419  -0.517  -0.016  1.00  0.00           C  
HETATM    9  N2  UNL     1       1.263  -0.640   0.633  1.00  0.00           N  
HETATM   10  H1  UNL     1      -2.705  -1.741   0.509  1.00  0.00           H  
HETATM   11  H2  UNL     1      -1.180  -0.033   1.488  1.00  0.00           H  
HETATM   12  H3  UNL     1      -1.116   1.620   0.744  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.703   1.836  -1.476  1.00  0.00           H  
HETATM   14  H5  UNL     1       3.314  -1.132   0.178  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.967  -1.267   1.387  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   10
CONECT    4    5   11   12
CONECT    5    6    6    9
CONECT    6    7   13
CONECT    7    8    8
CONECT    8    9   14
CONECT    9   15
END
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SMILES for HMDB0002024 (Imidazoleacetic acid)

OC(=O)CC1=CN=CN1
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INCHI for HMDB0002024 (Imidazoleacetic acid)

InChI=1S/C5H6N2O2/c8-5(9)1-4-2-6-3-7-4/h2-3H,1H2,(H,6,7)(H,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC5H6N2O2
Average Molecular Weight126.1133
Monoisotopic Molecular Weight126.042927446
IUPAC Name2-(1H-imidazol-5-yl)acetic acid
Traditional NameIMAC
CAS Registry Number645-65-8
SMILES
OC(=O)CC1=CN=CN1
InChI Identifier
InChI=1S/C5H6N2O2/c8-5(9)1-4-2-6-3-7-4/h2-3H,1H2,(H,6,7)(H,8,9)
InChI KeyPRJKNHOMHKJCEJ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as imidazolyl carboxylic acids and derivatives. These are organic compounds containing a carboxylic acid chain (of at least 2 carbon atoms) linked to an imidazole ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzoles
Sub ClassImidazoles
Direct ParentImidazolyl carboxylic acids and derivatives
Alternative Parents
Substituents
  • Imidazolyl carboxylic acid derivative
  • Heteroaromatic compound
  • Azacycle
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+MetCCS_train_pos123.05130932474
[M+H]+Not Available124.8http://allccs.zhulab.cn/database/detail?ID=AllCCS00000475
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030508
KNApSAcK IDNot Available
Chemspider ID86856
KEGG Compound IDC02835
BioCyc ID4-IMIDAZOLEACETATE
BiGG ID40666
Wikipedia LinkNot Available
METLIN ID6445
PubChem Compound96215
PDB IDNot Available
ChEBI ID16974
Food Biomarker OntologyNot Available
VMH IDIM4AC
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceMadsen Christian; Jensen Anders A; Liljefors Tommy; Kristiansen Uffe; Nielsen Birgitte; Hansen Camilla P; Larsen Mogens; Ebert Bjarke; Bang-Andersen Benny; Krogsgaard-Larsen Povl; Frolund Bente 5-Substituted imidazole-4-acetic acid analogues: synthesis, modeling, and pharmacological characterization of a series of novel gamma-aminobutyric acid(C) receptor agonists. Journal of medicinal chemistry (2007), 50(17), 4147-61.
Material Safety Data Sheet (MSDS)Download (PDF)
General References

Enzymes

Enzyme Details
1. 4-trimethylaminobutyraldehyde dehydrogenase
General function:
Involved in oxidoreductase activity
Specific function:
Converts gamma-trimethylaminobutyraldehyde into gamma-butyrobetaine. Catalyzes the irreversible oxidation of a broad range of aldehydes to the corresponding acids in an NAD-dependent reaction.
Gene Name:
ALDH9A1
Uniprot ID:
P49189
Molecular weight:
56291.485
Reactions
Imidazole-4-acetaldehyde + NAD + Water → Imidazoleacetic acid + NADH + Hydrogen Iondetails
Enzyme Details
2. Alpha-aminoadipic semialdehyde dehydrogenase
General function:
Involved in oxidoreductase activity
Specific function:
Multifunctional enzyme mediating important protective effects. Metabolizes betaine aldehyde to betaine, an important cellular osmolyte and methyl donor. Protects cells from oxidative stress by metabolizing a number of lipid peroxidation-derived aldehydes. Involved in lysine catabolism.
Gene Name:
ALDH7A1
Uniprot ID:
P49419
Molecular weight:
58486.74
Reactions
Imidazole-4-acetaldehyde + NAD + Water → Imidazoleacetic acid + NADH + Hydrogen Iondetails
Enzyme Details
3. Aldehyde dehydrogenase family 1 member A3
General function:
Involved in oxidoreductase activity
Specific function:
Recognizes as substrates free retinal and cellular retinol-binding protein-bound retinal. Seems to be the key enzyme in the formation of an RA gradient along the dorso-ventral axis during the early eye development and also in the development of the olfactory system (By similarity).
Gene Name:
ALDH1A3
Uniprot ID:
P47895
Molecular weight:
56107.995
Enzyme Details
4. Aldehyde dehydrogenase, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
ALDH2
Uniprot ID:
P05091
Molecular weight:
56380.93
Reactions
Imidazole-4-acetaldehyde + NAD + Water → Imidazoleacetic acid + NADH + Hydrogen Iondetails
Enzyme Details
5. Fatty aldehyde dehydrogenase
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the oxidation of long-chain aliphatic aldehydes to fatty acids. Active on a variety of saturated and unsaturated aliphatic aldehydes between 6 and 24 carbons in length. Responsible for conversion of the sphingosine 1-phosphate (S1P) degradation product hexadecenal to hexadecenoic acid.
Gene Name:
ALDH3A2
Uniprot ID:
P51648
Molecular weight:
54847.36
Reactions
Imidazole-4-acetaldehyde + NAD + Water → Imidazoleacetic acid + NADH + Hydrogen Iondetails
Enzyme Details
6. Aldehyde dehydrogenase X, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
ALDHs play a major role in the detoxification of alcohol-derived acetaldehyde. They are involved in the metabolism of corticosteroids, biogenic amines, neurotransmitters, and lipid peroxidation.
Gene Name:
ALDH1B1
Uniprot ID:
P30837
Molecular weight:
57248.96
Reactions
Imidazole-4-acetaldehyde + NAD + Water → Imidazoleacetic acid + NADH + Hydrogen Iondetails