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Showing metabocard for Hydantoin (HMDB0253235)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 11:33:43 UTC
Update Date2021-10-01 22:01:26 UTC
HMDB IDHMDB0253235
Secondary Accession NumbersNone
Metabolite Identification
Common NameHydantoin
DescriptionHydantoin, also known as glycolylurea, belongs to the class of organic compounds known as imidazoles. Imidazoles are compounds containing an imidazole ring, which is an aromatic five-member ring with two nitrogen atoms at positions 1 and 3, and three carbon atoms. Hydantoin has been detected, but not quantified in, several different foods, such as evening primroses (Oenothera biennis), herbs and spices, chia (Salvia hispanica), chinese water chestnuts (Eleocharis dulcis), and chicory leaves (Cichorium intybus var. foliosum). This could make hydantoin a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on Hydantoin. This compound has been identified in human blood as reported by (PMID: 31557052 ). Hydantoin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Hydantoin is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0253235 (Hydantoin)

  Mrv0541 02241221452D          

  7  7  0  0  0  0            999 V2000
   -0.7336    0.5055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6955    0.5055    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7336   -0.3193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3151    1.0909    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6955   -0.3193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0190   -0.7336    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4101   -0.7336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  2  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  7  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
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3D MOL for HMDB0253235 (Hydantoin)

HMDB0253235
     RDKit          3D
Hydantoin
 11 11  0  0  0  0  0  0  0  0999 V2000
   -1.1915    2.1130    0.2930 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5093    1.0815    0.0562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0433   -0.2636   -0.3072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0501   -1.1538    0.2310 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2074   -0.4912    0.1755 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3497   -1.0041    0.2129 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8980    0.9084    0.0661 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0563   -0.4367    0.0825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9912   -0.3214   -1.4202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2059   -2.1362    0.6087 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5926    1.7041    0.0016 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  2  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  7 11  1  0
M  END
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3D SDF for HMDB0253235 (Hydantoin)

  Mrv0541 02241221452D          

  7  7  0  0  0  0            999 V2000
   -0.7336    0.5055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6955    0.5055    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7336   -0.3193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3151    1.0909    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6955   -0.3193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0190   -0.7336    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4101   -0.7336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  2  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  7  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253235

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CNC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C3H4N2O2/c6-2-1-4-3(7)5-2/h1H2,(H2,4,5,6,7)

> <INCHI_KEY>
WJRBRSLFGCUECM-UHFFFAOYSA-N

> <FORMULA>
C3H4N2O2

> <MOLECULAR_WEIGHT>
100.0761

> <EXACT_MASS>
100.027277382

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
8.21974966978361

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
imidazolidine-2,4-dione

> <ALOGPS_LOGP>
-1.47

> <JCHEM_LOGP>
-1.4502204676666666

> <ALOGPS_LOGS>
-0.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.860764571723223

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.678378016311395

> <JCHEM_PKA_STRONGEST_BASIC>
-8.670979225740245

> <JCHEM_POLAR_SURFACE_AREA>
58.2

> <JCHEM_REFRACTIVITY>
21.046100000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.68e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
hydantoin

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0253235 (Hydantoin)

HMDB0253235
     RDKit          3D
Hydantoin
 11 11  0  0  0  0  0  0  0  0999 V2000
   -1.1915    2.1130    0.2930 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5093    1.0815    0.0562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0433   -0.2636   -0.3072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0501   -1.1538    0.2310 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2074   -0.4912    0.1755 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3497   -1.0041    0.2129 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8980    0.9084    0.0661 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0563   -0.4367    0.0825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9912   -0.3214   -1.4202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2059   -2.1362    0.6087 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5926    1.7041    0.0016 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  2  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  7 11  1  0
M  END
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PDB for HMDB0253235 (Hydantoin)

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  C   UNK     0      -1.369   0.944   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.298   0.944   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -1.369  -0.596   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -2.455   2.036   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.298  -0.596   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -0.035  -1.369   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       2.632  -1.369   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1                                                            
CONECT    5    2    7    6                                                  
CONECT    6    3    5                                                       
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0253235 (Hydantoin)

COMPND    HMDB0253235
HETATM    1  O1  UNL     1      -1.192   2.113   0.293  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.509   1.081   0.056  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.043  -0.264  -0.307  1.00  0.00           C  
HETATM    4  N1  UNL     1      -0.050  -1.154   0.231  1.00  0.00           N  
HETATM    5  C3  UNL     1       1.207  -0.491   0.176  1.00  0.00           C  
HETATM    6  O2  UNL     1       2.350  -1.004   0.213  1.00  0.00           O  
HETATM    7  N2  UNL     1       0.898   0.908   0.066  1.00  0.00           N  
HETATM    8  H1  UNL     1      -2.056  -0.437   0.082  1.00  0.00           H  
HETATM    9  H2  UNL     1      -0.991  -0.321  -1.420  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.206  -2.136   0.609  1.00  0.00           H  
HETATM   11  H4  UNL     1       1.593   1.704   0.002  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    8    9
CONECT    4    5   10
CONECT    5    6    6    7
CONECT    7   11
END
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SMILES for HMDB0253235 (Hydantoin)

O=C1CNC(=O)N1
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INCHI for HMDB0253235 (Hydantoin)

InChI=1S/C3H4N2O2/c6-2-1-4-3(7)5-2/h1H2,(H2,4,5,6,7)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2,4(3H,5H)-ImidazoledioneChEBI
2,4-ImidazolidinedioneChEBI
GlycolylureaChEBI
Imidazole-2,4(3H,5H)-dioneChEBI
Imidazolidine-2,4-dioneMeSH
Chemical FormulaC3H4N2O2
Average Molecular Weight100.0761
Monoisotopic Molecular Weight100.027277382
IUPAC Nameimidazolidine-2,4-dione
Traditional Namehydantoin
CAS Registry NumberNot Available
SMILES
O=C1CNC(=O)N1
InChI Identifier
InChI=1S/C3H4N2O2/c6-2-1-4-3(7)5-2/h1H2,(H2,4,5,6,7)
InChI KeyWJRBRSLFGCUECM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as imidazoles. Imidazoles are compounds containing an imidazole ring, which is an aromatic five-member ring with two nitrogen atoms at positions 1 and 3, and three carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzoles
Sub ClassImidazoles
Direct ParentImidazoles
Alternative Parents
Substituents
  • Imidazole
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB004274
KNApSAcK IDC00038953
Chemspider ID9612
KEGG Compound IDC05146
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkHydantoin
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID27612
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 References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Enzymes

Enzyme Details
1. Endonuclease 8-like 3
General function:
Not Available
Specific function:
DNA glycosylase which prefers single-stranded DNA (ssDNA), or partially ssDNA structures such as bubble and fork structures, to double-stranded DNA (dsDNA) (PubMed:20185759, PubMed:22065741, PubMed:22569481, PubMed:22959434, PubMed:23305905, PubMed:23313161). Mediates interstrand cross-link repair in response to replication stress: acts by mediating DNA glycosylase activity, cleaving one of the two N-glycosyl bonds comprising the interstrand cross-link, which avoids the formation of a double-strand break but generates an abasic site that is bypassed by translesion synthesis polymerases (By similarity). In vitro, displays strong glycosylase activity towards the hydantoin lesions spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh) in both ssDNA and dsDNA; also recognizes FapyA, FapyG, 5-OHU, 5-OHC, 5-OHMH, Tg and 8-oxoA lesions in ssDNA (PubMed:20185759, PubMed:22065741, PubMed:22569481, PubMed:22959434, PubMed:23305905, PubMed:23313161). No activity on 8-oxoG detected (PubMed:20185759, PubMed:22065741, PubMed:22569481, PubMed:22959434, PubMed:23305905, PubMed:23313161). Also shows weak DNA-(apurinic or apyrimidinic site) lyase activity (PubMed:20185759, PubMed:22065741, PubMed:22569481, PubMed:22959434, PubMed:23305905, PubMed:23313161). In vivo, appears to be the primary enzyme involved in removing Sp and Gh from ssDNA in neonatal tissues (PubMed:20185759, PubMed:22065741, PubMed:22569481, PubMed:22959434, PubMed:23305905, PubMed:23313161).
Gene Name:
NEIL3
Uniprot ID:
Q8K203
Molecular weight:
67415.815
Enzyme Details
2. Allantoinase
General function:
Not Available
Specific function:
Catalyzes the conversion of allantoin (5-ureidohydantoin) to allantoic acid by hydrolytic cleavage of the five-member hydantoin ring.
Gene Name:
ALLB
Uniprot ID:
A1A8H7
Molecular weight:
49587.21
Enzyme Details
3. Allantoinase
General function:
Not Available
Specific function:
Catalyzes the conversion of allantoin (5-ureidohydantoin) to allantoic acid by hydrolytic cleavage of the five-member hydantoin ring.
Gene Name:
ALLB
Uniprot ID:
Q5PCG0
Molecular weight:
49886.51
Enzyme Details
4. Endonuclease 8-like 3
General function:
Not Available
Specific function:
DNA glycosylase which prefers single-stranded DNA (ssDNA), or partially ssDNA structures such as bubble and fork structures, to double-stranded DNA (dsDNA) (PubMed:12433996, PubMed:19170771, PubMed:22569481, PubMed:23755964). Mediates interstrand cross-link repair in response to replication stress: acts by mediating DNA glycosylase activity, cleaving one of the two N-glycosyl bonds comprising the interstrand cross-link, which avoids the formation of a double-strand break but generates an abasic site that is bypassed by translesion synthesis polymerases (By similarity). In vitro, displays strong glycosylase activity towards the hydantoin lesions spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh) in both ssDNA and dsDNA; also recognizes FapyA, FapyG, 5-OHU, 5-OHC, 5-OHMH, Tg and 8-oxoA lesions in ssDNA (PubMed:12433996, PubMed:19170771, PubMed:22569481, PubMed:23755964). No activity on 8-oxoG detected (PubMed:12433996, PubMed:19170771, PubMed:22569481, PubMed:23755964). Also shows weak DNA-(apurinic or apyrimidinic site) lyase activity (PubMed:12433996, PubMed:19170771, PubMed:22569481, PubMed:23755964). In vivo, appears to be the primary enzyme involved in removing Sp and Gh from ssDNA in neonatal tissues (PubMed:12433996, PubMed:19170771, PubMed:22569481, PubMed:23755964).
Gene Name:
NEIL3
Uniprot ID:
Q8TAT5
Molecular weight:
67768.55